# HG changeset patch # User iuc # Date 1618914466 0 # Node ID 7c86ceaf523cdfb7050e000d87a81f1c543323bb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb" diff -r 000000000000 -r 7c86ceaf523c hyphy_strike_ambigs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hyphy_strike_ambigs.xml Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,40 @@ + + + in a multiple alignment using HyPhy + + macros.xml + + + + + + + + + + + + + + + + + + + + + + 10.1093/bioinformatics/bti079 + + diff -r 000000000000 -r 7c86ceaf523c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,144 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $posteriorEstimationMethod.method != "Variational-Bayes" + --chains '$posteriorEstimationMethod.chains' + --chain-length '$posteriorEstimationMethod.chain_length' + --burn-in '$posteriorEstimationMethod.samples' + --samples '$posteriorEstimationMethod.samples_per_chain' + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/molbev/msz197 + + + + 2.5.31 + + + hyphy + + + + \${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI + &2 ; + else + cat errors.log >&2 ; + fi ; + fi ; + exit \$EC + ]]> + + + + diff -r 000000000000 -r 7c86ceaf523c scripts/annotator.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/annotator.bf Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,102 @@ +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/convenience/regexp.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); + +tags = { + "^Node" : "Internal" +}; + + + + +tree = trees.LoadAnnotatedTopology (TRUE); +ts = tree[^"terms.trees.newick_with_lengths"]; +root_node = io.PromptUserForString ("Root on this node"); + + + +Topology T = ts; +ts = RerootTree (T, root_node); +ACCEPT_ROOTED_TREES = FALSE; +Topology T = ts; +ACCEPT_ROOTED_TREES = TRUE; +Topology TR = ts; + + +NORMALIZE_SEQUENCE_NAMES = FALSE; +SetDialogPrompt ("File with the sequences to label as the in-clade"); +DataSet query = ReadDataFile (PROMPT_FOR_FILE); +GetString (seqNames,query,-1); + +label = io.PromptUserForString ("Use this label"); + + +for (s;in;seqNames) { + tags [s && 6] = label; +} + +reg_exp = Rows (tags); + + +node_labels = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (T,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labels[l] = tag; + } + } +} + +node_labelsR = {}; +for (_regexp_, _leaves_; in; regexp.PartitionByRegularExpressions (BranchName (TR,-1), reg_exp)) { + tag = tags[_regexp_]; + + if (tag != "Internal") { + + if (Abs (tag) == 0) { + tag = "Reference"; + } + + for (l; in; _leaves_) { + node_labelsR[l] = tag; + } + } +} + + +leaf_labels = node_labels; +node_labelsF = node_labels; +node_labels * ((trees.ParsimonyLabel ("T", node_labels))["labels"]); +node_labelsR * ((trees.ParsimonyLabel ("T", node_labelsR))["labels"]); +node_labelsF * ((trees.ParsimonyLabel ("T", node_labelsF))["labels"]); + +output_to = io.PromptUserForString ("Write output to this prefix"); + +fprintf (output_to + "labels.json", CLEAR_FILE, leaf_labels); +fprintf (output_to + "int.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate", "{}", FALSE)); +fprintf (output_to + "clade.nwk", CLEAR_FILE, tree.Annotate ("TR", "relabel_and_annotate_full", "{}", FALSE)); +fprintf (output_to + "full.nwk", CLEAR_FILE, tree.Annotate ("T", "relabel_and_annotate_full", "{}", FALSE)); + +function relabel_and_annotate (node_name) { + _label = ""; + if (node_labels / node_name && leaf_labels / node_name == FALSE) { + _label = "{" + node_labels[node_name] + "}"; + } + return node_name + _label; +} + +function relabel_and_annotate_full (node_name) { + _label = ""; + if (node_labelsR / node_name) { + _label = "{" + node_labelsR[node_name] + "}"; + } + return node_name + _label; +} diff -r 000000000000 -r 7c86ceaf523c scripts/strike-ambigs.bf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/strike-ambigs.bf Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,83 @@ +RequireVersion ("2.5.20"); + +LoadFunctionLibrary ("libv3/tasks/alignments.bf"); +LoadFunctionLibrary ("libv3/tasks/trees.bf"); +LoadFunctionLibrary ("libv3/UtilityFunctions.bf"); +LoadFunctionLibrary ("libv3/IOFunctions.bf"); +LoadFunctionLibrary ("libv3/convenience/math.bf"); + + + +filter.analysis_description = {terms.io.info : + " + Read an alignment of coding sequences and replace any ambiguous codons with ---. Write results to a new file in FASTA format, and report changed sequences to stdout + ", + terms.io.version : "0.1", + terms.io.reference : "TBD", + terms.io.authors : "Sergei L Kosakovsky Pond", + terms.io.contact : "spond@temple.edu", + terms.io.requirements : "An MSA" + }; + + +io.DisplayAnalysisBanner (filter.analysis_description); + +utility.SetEnvVariable ("NORMALIZE_SEQUENCE_NAMES", FALSE); + +KeywordArgument ("code", "Which genetic code should be used", "Universal"); +KeywordArgument ("alignment", "An in-frame codon alignment in one of the formats supported by HyPhy"); + +filter.in = alignments.PromptForGeneticCodeAndAlignment ("filter.dataset", "filter.input"); + +KeywordArgument ("output", ".fasta for compressed data", None); +filter.out = io.PromptUserForFilePath(".fasta for filtered data"); +fprintf (filter.out, CLEAR_FILE, KEEP_OPEN); + +GetDataInfo (filter.site_patterns, filter.input); + +filter.patter2site = {}; + + +for (i,j,v; in; filter.site_patterns) { + index = i+j; + if (filter.patter2site / v == FALSE ) { + filter.patter2site [v] = {}; + } + filter.patter2site [v] + index; +} + +GET_DATA_INFO_RETURNS_ONLY_THE_INDEX = TRUE; +COUNT_GAPS_IN_FREQUENCIES = FALSE; +filter.unique_patterns = utility.Array1D (filter.input.site_freqs); + +for (seq = 0; seq < filter.input.species; seq += 1) { + io.ReportProgressBar ("filter","Processing sequence " + (1+seq)); + codons = {1, filter.input.sites}; + codons [0] = ""; + GetString (seq_name, filter.input, seq); + GetDataInfo (seq_chars, filter.input, seq); + + filter.ambigs = 0; + + for (pattern = 0; pattern < filter.unique_patterns; pattern += 1) { + GetDataInfo (pattern_info, filter.input, seq, pattern); + if (pattern_info >= 0) { + codon_start = (filter.patter2site[pattern])[0] * 3; + codon = seq_chars [codon_start][codon_start+2]; + } else { + codon = "---"; + filter.ambigs += Abs (filter.patter2site [pattern]) + } + for (c; in; filter.patter2site [pattern] ) { + codons[c] = codon; + } + } + if (filter.ambigs > 0) { + fprintf (stdout, "\nStriking ", filter.ambigs, " codons that are incompletely resolved from " + seq_name + "\n"); + } + fprintf (filter.out,">",seq_name,"\n",Join ("", codons), "\n"); +} + +fprintf (filter.out,CLOSE_FILE); + + diff -r 000000000000 -r 7c86ceaf523c test-data/absrel-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,20 @@ +>Human +AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Chimp +GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Baboon +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>RhMonkey +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Cow +------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT +>Pig +---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT +>Horse +------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT +>Cat +---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC +>Mouse +---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC +>Rat +---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC diff -r 000000000000 -r 7c86ceaf523c test-data/absrel-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.097950); \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/absrel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/absrel-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,478 @@ +{ + "analysis":{ + "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", + "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models", + "contact":"spond@temple.edu", + "info":"aBSREL (Adaptive branch-site random effects likelihood)\n uses an adaptive random effects branch-site model framework\n to test whether each branch has evolved under positive selection,\n using a procedure which infers an optimal number of rate categories per branch.", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.2" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "Baseline MG94xREV":0.001816807585564731, + "Baseline MG94xREV omega ratio":0, + "Corrected P-value":1, + "Full adaptive model":0.001810407118394509, + "LRT":0, + "Nucleotide GTR":0.001678881906620672, + "Rate Distributions": [ +[0, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "original name":"Baboon", + "rate at which 2 nucleotides are changed instantly within a single codon":0 + }, + "Cat":{ + "Baseline MG94xREV":0.2286001363527903, + "Baseline MG94xREV omega ratio":1.403298474422089, + "Corrected P-value":1, + "Full adaptive model":0.1219386838393392, + "LRT":1.644967676056694, + "Nucleotide GTR":0.265904547400163, + "Rate Distributions": [ +[0.2130519766306851, 0.6352283641519592], + [2.628217450705319, 0.3647716358480408] + ], + "Rate classes":2, + "Uncorrected P-value":0.171730764045231, + "original name":"Cat", + "rate at which 2 nucleotides are changed instantly within a single codon":0 + }, + "Chimp":{ + "Baseline MG94xREV":0.001840311209746262, + "Baseline MG94xREV omega ratio":10000000000, + "Corrected P-value":1, + "Full adaptive model":0.001841979303044237, + "LRT":0.6159123786974305, + "Nucleotide GTR":0.001816713800925801, + "Rate Distributions": [ +[10000000000, 1] + ], + "Rate classes":1, + "Uncorrected P-value":0.3069983227523322, + "original name":"Chimp", + "rate at which 2 nucleotides are changed instantly within a single codon":0 + }, + "Cow":{ + "Baseline MG94xREV":0.2070244948790512, + "Baseline MG94xREV omega ratio":2.153434974462683, + "Corrected P-value":0.5006146299996015, + "Full adaptive model":0.1241125417707662, + "LRT":4.898194538953248, + "Nucleotide GTR":0.2481512612523618, + "Rate Distributions": [ +[0, 0.52318726440949], + [2.444056517734385, 0.47681273559051] + ], + "Rate classes":2, + "Uncorrected P-value":0.03128841437497509, + "original name":"Cow", + "rate at which 2 nucleotides are changed instantly within a single codon":0 + }, + "Horse":{ + "Baseline MG94xREV":0.190365915457708, + "Baseline MG94xREV omega ratio":1.182933895494305, + "Corrected P-value":1, + "Full adaptive model":0.0869489794025302, + "LRT":2.047309801283518, + "Nucleotide GTR":0.2090927256979082, + "Rate Distributions": [ +[0, 0.5397658078247131], + [1.633257246666139, 0.4602341921752869] + ], + "Rate classes":2, + "Uncorrected P-value":0.1382789032066179, + "original name":"Horse", + "rate at which 2 nucleotides are changed instantly within a single codon":0 + }, + "Human":{ + "Baseline MG94xREV":0, + "Baseline MG94xREV omega ratio":1, + "Corrected P-value":1, + "Full adaptive model":0, + "LRT":0, + "Nucleotide GTR":0, + "Rate Distributions": [ +[1, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "original name":"Human", + "rate at which 2 nucleotides are changed instantly within a single codon":0.0006106118725184574 + }, + "Mouse":{ + "Baseline MG94xREV":0.1083167307250788, + "Baseline MG94xREV omega ratio":0.5108576904540283, + "Corrected P-value":1, + "Full adaptive model":0.1078010043714489, + "LRT":0, + "Nucleotide GTR":0.1181001275359051, + "Rate Distributions": [ +[0.5087375113796073, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "original name":"Mouse", + "rate at which 2 nucleotides are changed instantly within a single codon":0.4244832903005548 + }, + "Node1":{ + "Baseline MG94xREV":0.2542393300501047, + "Baseline MG94xREV omega ratio":0.2997498382776075, + "Corrected P-value":1, + "Full adaptive model":0.2550466752020236, + "LRT":0, + "Nucleotide GTR":0.2767426965701868, + "Rate Distributions": [ +[0.2932817609633239, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "rate at which 2 nucleotides are changed instantly within a single codon":0.9114373463003921 + }, + "Node12":{ + "Baseline MG94xREV":0.01400815185374474, + "Baseline MG94xREV omega ratio":0.2754467062829232, + "Corrected P-value":1, + "Full adaptive model":0.01437973904273591, + "LRT":0, + "Nucleotide GTR":0.01784721909304638, + "Rate Distributions": [ +[0.3037614070859027, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "rate at which 2 nucleotides are changed instantly within a single codon":0.5084909616267814 + }, + "Node2":{ + "Baseline MG94xREV":0.0400106272595141, + "Baseline MG94xREV omega ratio":0.116408812566168, + "Corrected P-value":1, + "Full adaptive model":0.03991940069030483, + "LRT":0, + "Nucleotide GTR":0.06613304839358287, + "Rate Distributions": [ +[0.1193993042178124, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "rate at which 2 nucleotides are changed instantly within a single codon":9.28646275825122 + }, + "Node3":{ + "Baseline MG94xREV":0.08548068002443369, + "Baseline MG94xREV omega ratio":1.293385437932658, + "Corrected P-value":1, + "Full adaptive model":0.08590119038008139, + "LRT":0.1383887036890883, + "Nucleotide GTR":0.09881178513658169, + "Rate Distributions": [ +[1.330576641567385, 1] + ], + "Rate classes":1, + "Uncorrected P-value":0.4219212196398351, + "rate at which 2 nucleotides are changed instantly within a single codon":0.8390789546113498 + }, + "Node8":{ + "Baseline MG94xREV":0.09463393920061362, + "Baseline MG94xREV omega ratio":1.862136443854597, + "Corrected P-value":1, + "Full adaptive model":0.0958035263641453, + "LRT":0.7150293976401372, + "Nucleotide GTR":0.1062333225692588, + "Rate Distributions": [ +[1.883870769808856, 1] + ], + "Rate classes":1, + "Uncorrected P-value":0.2893795680778183, + "rate at which 2 nucleotides are changed instantly within a single codon":0.512238843416092 + }, + "Node9":{ + "Baseline MG94xREV":0.02846111726225027, + "Baseline MG94xREV omega ratio":0.4321055128385307, + "Corrected P-value":1, + "Full adaptive model":0.02810856974543091, + "LRT":0, + "Nucleotide GTR":0.02566185438854229, + "Rate Distributions": [ +[0.4185836885800617, 1] + ], + "Rate classes":1, + "Uncorrected P-value":1, + "rate at which 2 nucleotides are changed instantly within a single codon":0 + }, + "Pig":{ + "Baseline MG94xREV":0.1782835053555321, + "Baseline MG94xREV omega ratio":1.275728452678247, + "Corrected P-value":1, + "Full adaptive model":0.1729188354138871, + "LRT":0.3324036585026988, + "Nucleotide GTR":0.1871760137183495, + "Rate Distributions": [ +[1.235108129487059, 1] + ], + "Rate classes":1, + "Uncorrected P-value":0.3669120164240152, + "original name":"Pig", + "rate at which 2 nucleotides are changed instantly within a single codon":0.1143447431158695 + }, + "Rat":{ + "Baseline MG94xREV":0.06315403896300904, + "Baseline 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selection":{ + "order":5, + "timer":112 + } + } +} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-in1.fa.gz Binary file test-data/annotate-in1.fa.gz has changed diff -r 000000000000 -r 7c86ceaf523c test-data/annotate-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotate-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ 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test-data/bgm-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,20 @@ +>Human +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Chimp +GCACAATTCAGAAAAGAGAAAGAGACTTTC +>Baboon +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>RhMonkey +GCACAATTCAGAAAAGAGAAGGAGACTTTC +>Cow +GCACGAATAAAGAAAGATATGCCACTTCAC +>Pig +GCAGAATTTAAAAAAAACAAAGAAACTCAC +>Horse +GCAAAATTCAAAAATGGCAGTATGACTTTC +>Cat +GCGAGGTTCCAAATTAGCAACAAGCCTAAG +>Mouse +GCAGAGTTTAAAAGGAAGAAGCCACCTTTT +>Rat +GCCGAGTTTAAAAGGAAGATGAAGCCTTTT diff -r 000000000000 -r 7c86ceaf523c test-data/bgm-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.097950); diff -r 000000000000 -r 7c86ceaf523c test-data/bgm-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bgm-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,168 @@ +{ + "MLE":{ + "content": [ +[2, 3, 0.02851572177464722, 0.01992394838090668, 0.04843967015555389, 4, 3, 1], + [2, 4, 0.2913031811286725, 0.1581095173619919, 0.4494126984906644, 4, 2, 2], + [2, 5, 0.04313828130286183, 0.09337388689236253, 0.1365121681952244, 4, 3, 2], + [2, 6, 0.05037434713194238, 0.07113225549859428, 0.1215066026305367, 4, 6, 3], + [2, 7, 0.2804886800096655, 0.2001828066808252, 0.4806714866904907, 4, 4, 3], + [2, 8, 0.07183821900324161, 0.1469389589305462, 0.2187771779337878, 4, 5, 3], + [2, 9, 0.03082407077478325, 0.09900473652454521, 0.1298288072993285, 4, 3, 2], + [2, 10, 0.02245776059232202, 0.02955557233236829, 0.05201333292469031, 4, 3, 1], + [3, 4, 0.03717045364745913, 0.02520976460488304, 0.06238021825234218, 3, 2, 0], + [3, 5, 0.02873335174526813, 0.03479214292405394, 0.06352549466932207, 3, 3, 1], + [3, 6, 0.1236923855363388, 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0.1329905971978248, 3, 4, 2], + [5, 8, 0.1895195673806065, 0.2930011407919719, 0.4825207081725784, 3, 5, 3], + [5, 9, 0.1148199627842869, 0.1105571269028783, 0.2253770896871652, 3, 3, 2], + [5, 10, 0.1270434887308012, 0.1100230063742557, 0.2370664951050569, 3, 3, 2], + [6, 7, 0.09069770755435493, 0.0484084497358865, 0.1391061572902414, 6, 4, 3], + [6, 8, 0.1325890592140632, 0.1385237411340729, 0.2711128003481361, 6, 5, 4], + [6, 9, 0.1237432424538594, 0.1610336810828299, 0.2847769235366894, 6, 3, 3], + [6, 10, 0.2074649804257667, 0.132053108013182, 0.3395180884389487, 6, 3, 3], + [7, 8, 0.0894441901425615, 0.1431622704391284, 0.2326064605816899, 4, 5, 3], + [7, 9, 0.06037024754303832, 0.114173814968622, 0.1745440625116604, 4, 3, 2], + [7, 10, 0.02455907863678367, 0.02700169365828593, 0.0515607722950696, 4, 3, 1], + [8, 9, 0.2356164682007381, 0.275411073609017, 0.5110275418097552, 5, 3, 3], + [8, 10, 0.05927356969559661, 0.02598780235339034, 0.08526137204898694, 5, 3, 2], + [9, 10, 0.1776480482199785, 0.09671451255218226, 0.2743625607721607, 3, 3, 2] + ], + "headers": [ +["Site 1", "Index of site 1"], + ["Site 2", "Index of site 2"], + ["P [Site 1 –> Site 2]", "Probability that site 2 is conditionally dependent on site 1"], + ["P [Site 2 –> Site 1]", "Probability that site 1 is conditionally dependent on site 2"], + ["P [Site 1 <–> Site 2]", "Probability that sites 1 and 2 are not conditionally independent"], + ["Site 1 subs", "Substitution counts inferred for Site 1"], + ["Site 2 subs", "Substitution counts inferred for Site 2"], + ["Shared subs", "Substitutions shared by both sites"] + ] + }, + "analysis":{ + "authors":"Art FY Poon, Fraser I Lewis, Simon DW Frost and Sergei L Kosakovsky Pond", + "citation":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models (2008). _Bioinformatics_ 24(17): 1949-1950", + "contact":"apoon42@uwo.ca", + "info":"BGM (Bayesian Graphical Model) uses a maximum likelihood ancestral state reconstruction to\nmap substitution (non-synonymous only for coding data) events to branches in the\nphylogeny and then analyzes the joint distribution of the\nsubstitution map using a Bayesian graphical model (network).\nNext, a Markov chain Monte Carlo analysis is used to generate\na random sample of network structures from the posterior\ndistribution given the data. Each node in the network\nrepresents a codon site in the alignment, and links (edges)\nbetween nodes indicate high posterior support for correlated\nsubstitutions at the two sites over time, which implies coevolution.", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"1.1" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Cat":{ + "models.codon.MG_REV.ModelDescription":0.8288168941011919 + }, + "Chimp":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Cow":{ + "models.codon.MG_REV.ModelDescription":0.8164924147537205 + }, + "Horse":{ + "models.codon.MG_REV.ModelDescription":0.2841592907567805 + }, + "Human":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Mouse":{ + "models.codon.MG_REV.ModelDescription":0.1035113121392619 + }, + "Node1":{ + "models.codon.MG_REV.ModelDescription":0.5236339695213962 + }, + "Node12":{ + "models.codon.MG_REV.ModelDescription":0 + }, + "Node2":{ + 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name":"/tmp/tmp_Fhyr9/job_working_directory/000/3/working/./bgm_input.fa", + "number of sequences":10, + "number of sites":10, + "trees":{ + "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)" + } + }, + "settings":{ + "burn-in":10000, + "data-type":"codon", + "max-parents":1, + "min-subs":1, + "samples":100, + "steps":100000, + "threshold":0.5 + }, + "tested":0, + "timers":{ + "Baseline fit":{ + "order":1, + "timer":3 + }, + "Network inference":{ + "order":2, + "timer":0 + }, + "Overall":{ + "order":0, + "timer":3 + } + } +} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/busted-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busted-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,394 @@ +{ + "Evidence Ratios":{ + "constrained": 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explore which individual sites may have been subject to selection. v2.0 adds support for synonymous rate variation, \nand relaxes the test statistic to 0.5 (chi^2_0 + chi^2_2). Version 2.1 adds a grid search for the initial starting point.\nVersion 2.2 changes the grid search to LHC, and adds an initial search phase to use adaptive Nedler-Mead. Version 3.0 implements the option\nfor branch-site variation in synonymous substitution rates\n", + "requirements":"in-frame codon alignment and a phylogenetic tree (optionally annotated with {})", + "version":"3.0" + }, + "background":0, + "branch attributes":{ + "0":{ + "Baboon":{ + "MG94xREV with separate rates for branch sets":0.001771850913718116, + "Nucleotide GTR":0.00167976779100812, + "constrained":0.0005055252388761481, + "original name":"Baboon", + "unconstrained":0.0005398732671668005 + }, + "Cat":{ + "MG94xREV with separate rates for branch sets":0.2738959056554072, + "Nucleotide GTR":0.266075486389923, + "constrained":0.1152712488116292, + "original name":"Cat", + "unconstrained":0.120218071527276 + }, + "Chimp":{ + "MG94xREV with separate rates for branch sets":0.001827968855137289, + "Nucleotide GTR":0.001817801565830578, + "constrained":0.0006181497274348637, + "original name":"Chimp", + "unconstrained":0.0006183542388399873 + }, + "Cow":{ + "MG94xREV with separate 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internal branches"], + ["P-value (overall)", "P-value for the test that non-synonymous rates differ between any of the selected groups: leaf,internal"], + ["Q-value (overall)", "Q-value for the test that non-synonymous rates differ between any of the selected groups: leaf,internal"], + ["Permutation p-value", "Label permutation test for significant sites"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale beta-alpha"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Steven Weaver", + "citation":"TBD", + "contact":"spond@temple.edu", + "help":"http://www.hyphy.org/methods/other/contrast-fel/", + "info":"Contrast-FEL (Fixed Effects Likelihood) investigates whether or not selective pressures differ between two or more sets of\n branches at a site. Site-specific synonymous (alpha) and non-synonymous (beta, one per branch set) substitution rates are estimated\n and then beta rates are tested for equality at each site. LRT and permutation tests ar used to assess significance at each site, and FDR is applied alignment wide to call sites with different selective profiles", + "requirements":"in-frame codon alignment and a phylogenetic tree; only single partition data are supported", + "version":"0.5" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "Global MG94xREV":0.00174723192666697, + "Nucleotide GTR":0.001680040630127455, + "original name":"Baboon" + }, + "Cat":{ + "Global MG94xREV":0.2766003372098463, + "Nucleotide GTR":0.2660909938917123, + "original name":"Cat" + }, + "Chimp":{ + "Global MG94xREV":0.001830140161785499, + "Nucleotide GTR":0.001818373670119325, + "original name":"Chimp" + }, + "Cow":{ + "Global MG94xREV":0.2512572530183805, + "Nucleotide GTR":0.2481025999892287, + "original name":"Cow" + }, + "Horse":{ + "Global MG94xREV":0.2146526643681058, + "Nucleotide GTR":0.2090310577070883, + "original name":"Horse" + }, + "Human":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"Human" + }, + "Mouse":{ + "Global MG94xREV":0.1196529267467225, + "Nucleotide GTR":0.1180171198334285, + "original name":"Mouse" + }, + "Node1":{ + "Global MG94xREV":0.2867621941821688, + "Nucleotide GTR":0.2767237570684924 + }, + "Node12":{ + "Global MG94xREV":0.01761131890611436, + "Nucleotide GTR":0.01784803874223016 + }, + "Node2":{ + "Global MG94xREV":0.06219797728198844, + "Nucleotide GTR":0.06613162123865737 + }, + "Node3":{ + "Global MG94xREV":0.09597116861714063, + "Nucleotide GTR":0.09886326330774685 + }, + "Node8":{ + "Global MG94xREV":0.1106045193971755, + "Nucleotide GTR":0.106239268140425 + }, + "Node9":{ + "Global MG94xREV":0.02619890351105751, + "Nucleotide GTR":0.02566573875750134 + }, + "Pig":{ + "Global MG94xREV":0.1934958194962019, + "Nucleotide GTR":0.1871893456388788, + "original name":"Pig" + }, + "Rat":{ + "Global MG94xREV":0.06790438491245605, + "Nucleotide GTR":0.06661283005976348, + "original name":"Rat" + }, + "RhMonkey":{ + "Global MG94xREV":0.003743023039574662, + "Nucleotide GTR":0.003775170135617877, + "original name":"RhMonkey" + } + }, + "attributes":{ + "Global MG94xREV":{ + "attribute type":"branch length", + "display order":1 + }, + "Nucleotide GTR":{ + "attribute type":"branch length", + "display order":0 + }, + "original name":{ + "attribute type":"node label", + "display order":-1 + } + } + }, + "data partitions":{ + "0":{ + "coverage": [ +[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186] + ], + "name":"fel.filter.default" + } + }, + "fits":{ + "Global MG94xREV":{ + "AIC-c":6991.186386461754, + "Equilibrium frequencies": [ +[0.04876086397632926], + [0.03982224127745371], + [0.0494959405650269], + [0.04152830682371345], + [0.01810345074594235], + [0.01478480742075003], + [0.01837636270304883], + [0.01541821854326533], + [0.01892910005547028], + [0.01545910240515689], + [0.01921445878706794], + [0.01612140169177368], + [0.02829747763884322], + [0.02311011106415996], + [0.02872406592369408], + [0.02410019507229243], + [0.01663805943190806], + [0.01358804506433061], + [0.01688888041768248], + [0.01417018446135155], + [0.006177213955434187], + [0.005044834822351987], + [0.006270336287397383], + [0.00526096577332031], + 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Distributions":{ + "non-synonymous/synonymous rate ratio for *internal*": [ +[0.6757243377045866, 1] + ], + "non-synonymous/synonymous rate ratio for *leaf*": [ +[1.251739840537981, 1] + ] + }, + "display order":1, + "estimated parameters":32 + }, + "Nucleotide GTR":{ + "AIC-c":7112.857310169033, + "Equilibrium frequencies": [ +[0.3592490842490842], + [0.181959706959707], + [0.240018315018315], + [0.2187728937728937] + ], + "Log Likelihood":-3532.32122446679, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.5501644800943087, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.2647746107611847, + "Substitution rate from nucleotide C to nucleotide G":0.4917423221832032, + "Substitution rate from nucleotide C to nucleotide T":1.02837595903795, + "Substitution rate from nucleotide G to nucleotide T":0.304509117524575 + }, + "display order":0, + "estimated parameters":24 + } + }, + "input":{ + "file name":"/tmp/tmp29yw9zzo/job_working_directory/000/3/working/cfel_input.fa", + "number of sequences":10, + "number of sites":187, + "partition count":1, + "trees":{ + "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.08509899999999999,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)" + } + }, + "tested":{ + "0":{ + "Baboon":"leaf", + "Cat":"leaf", + "Chimp":"leaf", + "Cow":"leaf", + "Horse":"leaf", + "Human":"leaf", + "Mouse":"leaf", + "Node1":"internal", + "Node12":"internal", + "Node2":"internal", + "Node3":"internal", + "Node8":"internal", + "Node9":"internal", + "Pig":"leaf", + "Rat":"leaf", + "RhMonkey":"leaf" + } + }, + "timers":{ + "FEL analysis":{ + "order":2, + "timer":180 + }, + "Model fitting":{ + "order":1, + "timer":13 + }, + "Total time":{ + "order":0, + "timer":193 + } + } +} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/conv-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,22 @@ +>epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGACG +>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + +>gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4 +CTTGTTTTTTTTTTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGATTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCTATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA + +>gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1 +ATGTATGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGTAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA + +>gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA + +>gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTTATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACCACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATTGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA + +>gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA + +>REFERENCE +ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/conv-out1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/conv-out1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,27 @@ +#NEXUS + +BEGIN TAXA; + DIMENSIONS NTAX = 8; + TAXLABELS + 'epi_isl_1041406_hCoV_19_USA_NY_PRL_2021_02_08_05H12_2021' 'epi_isl_1041403_hCoV_19_USA_NY_PRL_2021_02_08_05H08_2021' 'gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4' 'gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1' 'gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3' 'gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1' 'gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1' 'REFERENCE' ; +END; + +BEGIN CHARACTERS; + DIMENSIONS NCHAR = 1273; + FORMAT + DATATYPE = PROTEIN + GAP=- + MISSING=? + NOLABELS + ; + +MATRIX + ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ET + ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? + LVFFFVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGLSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDLSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT + MYVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPVTVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT + MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT + MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFYNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT + MLVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTLFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNHPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT + MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT; +END; \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/fade-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,50 @@ +>Human +KEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Chimp +EEITNALETWGALGQDINLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFKEKDTY +KLFKNGTLKIKH-LKTDDQDIYKVSIYDTKGKNVLEKIFDLKIQERVSKPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVS +CPEKGLD +>Baboon +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIKWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKIKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTDPELNLYQDGKHLK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>RhMonkey +KEIRNALETWGALGQDIDLDIPSFQMSDDIDDIRWEKTSDKKKIAQFRKEKETFEEKDAY +KLFKNGTLKXKH-LKIHDQDSYKVSIYDTKGKNVLEKTFDLKIQERVSEPKISWTCINTT +LTCEVMNGTXPELNLYQDGKHVK-LSQRVITHKWTTSLSAKFKCTAGNKVSKESRMETVS +CPEKGLD +>Cow +----ESIVVWGALDHDLNLDIPGFPRSDIVADIKWNR--NKNKIARIKKDMPLHNEMDKY +DMFTNGTLKIKT-LMRNDSGLYEVEVYDSNGVNLLSKKFDLKIQEMLSGPEINWICTNRT +VSCKVENGSNPKLQLFLNTTRVKQDHGKLITYTWNTRWNKTFKCVASNHVDSKVSIEIAV +CPDEGLD +>Pig +-----TEVVWGIVDQDINLDIPELSKHDNVDHIRWQK--NENKIAEFKKNKETHPVKDTY +MMLPNGTLRIKD-LKRDDEGIYKVTVYATDGKHMLERKFDLPILDGVSKPVISWSCADKT +VTCEVAEGSDPKLKLYVNKSTAREGRQKVILWKWNTKWSTLFKCVASNNASEQISMVTIS +CTGQGLD +>Horse +----KNITILGALERDINLDIPAFQMSEHVEDIQWSK--GKTKIAKFKNGSMTFQKDKTY +EVLKNGTLKIKH-LERIHEGTYKVDAYDSDGKNVLEETFHLSLLEMVSKPNISWSCTNTT +LTCEVTKGTDFELKLYLNGRMIQKSPRKVIVYKRASNQIASFKCTANNTVSEESSSVVIR +CTEKGLD +>Cat +---ANDDIVWGTLGQDINLDIPDSQ-GINIDDIHWEK--GKKKVARFQISNKPKNPDEKY +NVSMNGTLKIKH-LMLEDCDTYKVVIYDKDGKNVLDKTFQLKIQEKVSTPNIDWNCINKT +LVCKVSNGTDPELKLYVNGTSIKPVSSKFSTYRFINKQKILVNCTAENKVSKESDVKMIT +CSEKGLD +>Mouse +---RDNETIWGVLGHGITLNIPNFQMTDDIDEVRWVR--RGTLVAEFKRKKPPFLISETY +EVLANGSLKIKKPMMRNDSGTYNVMVYGTNGMTRLEKDLDVRILERVSKPMIHWECPNTT +LTCAVLQGTDFELKLYQGETLLNSLPQKNMSYQW-TNLNAPFKCEAINPVSKESKMEVVN +CPEKGLS +>Rat +---RDSGTVWGALGHGINLNIPNFQMTDDIDEVRWER--GSTLVAEFKRKMKPFLKSGAF +EILANGDLKIKN-LTRDDSGTYNVTVYSTNGTRILDKALDLRILEMVSKPMIYWECSNAT +LTCEVLEGTDVELKLYQGKEHLRSLRQKTMSYQW-TNLRAPFKCKAVNRVSQESEMEVVN +CPEKGLP diff -r 000000000000 -r 7c86ceaf523c test-data/fade-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +(((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958):0.1,Mouse:0.097950); diff -r 000000000000 -r 7c86ceaf523c test-data/fade-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fade-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,4281 @@ +{ + "MLE":{ + "content":{ + "A":{ + "0": [ +[11.51603702583788, 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to test whether or not a subset of sites in a protein alignment\n evolve towards a particular residue along a subset of branches at accelerated rates compared to reference model.\n FADE uses a random effects model and latent Dirichlet allocation (LDA) - inspired approximation methods to allocate sites to rate classes.", + "requirements":"A protein alignment and a **rooted** phylogenetic tree (optionally annotated with {})", + "version":"0.2" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "GTR":0, + "original name":"Baboon" + }, + "Cat":{ + "GTR":0.5479738108231806, + "original name":"Cat" + }, + "Chimp":{ + "GTR":0.005354406956230157, + "original name":"Chimp" + }, + "Cow":{ + "GTR":0.5217716656054335, + "original name":"Cow" + }, + "Horse":{ + "GTR":0.3639593662085931, + "original name":"Horse" + }, + "Human":{ + "GTR":0, + "original name":"Human" + }, + "Mouse":{ + "GTR":0.1538063185305938, + "original name":"Mouse" + }, + "Node1":{ + "GTR":0.03774939091948738 + }, + "Node10":{ 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analysis":{ + "order":2, + "timer":2 + }, + "Residue C analysis":{ + "order":3, + "timer":1 + }, + "Residue D analysis":{ + "order":4, + "timer":1 + }, + "Residue E analysis":{ + "order":5, + "timer":1 + }, + "Residue F analysis":{ + "order":6, + "timer":2 + }, + "Residue G analysis":{ + "order":7, + "timer":1 + }, + "Residue H analysis":{ + "order":8, + "timer":2 + }, + "Residue I analysis":{ + "order":9, + "timer":1 + }, + "Residue K analysis":{ + "order":10, + "timer":2 + }, + "Residue L analysis":{ + "order":11, + "timer":1 + }, + "Residue M analysis":{ + "order":12, + "timer":2 + }, + "Residue N analysis":{ + "order":13, + "timer":2 + }, + "Residue P analysis":{ + "order":14, + "timer":1 + }, + "Residue Q analysis":{ + "order":15, + "timer":2 + }, + "Residue R analysis":{ + "order":16, + "timer":2 + }, + "Residue S analysis":{ + "order":17, + "timer":2 + }, + "Residue T analysis":{ + "order":18, + "timer":2 + }, + "Residue V analysis":{ + "order":19, + "timer":2 + }, + "Residue W analysis":{ + "order":20, + "timer":2 + }, + "Residue Y analysis":{ + "order":21, + "timer":2 + } + } +} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/fel-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fel-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,450 @@ +{ + "analysis":{ + "info":"FEL (Fixed Effects Likelihood)\n estimates site-wise synonymous (α) and non-synonymous (β) rates, and\n uses a likelihood ratio test to determine if beta &neq; alpha at a site.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "version":"2.00", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "contact":"spond@temple.edu", + "requirements":"in-frame codon alignment and a phylogenetic tree" + }, + "input":{ + "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta", + "number of sequences":10, + "number of sites":187, + "partition count":1, + "trees":{ + 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+GCACATTACA-GTCAAATCCCTTCTCGTCCCC-ATGG-ATGACCCCCC-T +CAGAT-AGGGGTCCCTTGACCACCATCC \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/gard-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gard-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,318 @@ +{ + "analysis":{ + "authors":"Sergei L Kosakovsky Pond", + "citation":"**Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm**, _Mol Biol Evol 23(10), 1891–1901", + "contact":"spond@temple.edu", + "info":"GARD : Genetic Algorithms for Recombination Detection. Implements a heuristic\n approach to screening alignments of sequences for recombination, by using the CHC genetic algorithm to search for phylogenetic\n incongruence among different partitions of the data. The number of partitions is determined using a step-up procedure, while the\n placement of breakpoints is searched for with the GA. The best fitting model (based on c-AIC) is returned; and additional post-hoc\n tests run to distinguish topological incongruence from rate-variation.", + "requirements":"A sequence alignment.", + "version":"0.1" + }, + "baselineScore":8884.998566352424, + "breakpointData":{ + "0":{ + "bps": [ +[1, 461] + ], + 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AACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA AAGTAAACGGGCAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAG CCGAATGATGCTATCAATTTCGATAGTAATGGAAATTTCATTGCTCCAGA ATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCGATTATGAAAAGTG AATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG ATAAATTCTAGTATGCCATTCCACAACATACACCCTCTCACCGTCGGGGA ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTCGCGACTGGACTCA GAAATGCCCCTCAAAGAGAGGGAGGAAGAAAAAAGAGAGGACTATTTGGA GCCATAGCAGGGTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA TAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT TCCTAGATGTCTGGACTTATAACGCTGAACTTCTGGTTCTCATGGAAAAT GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGAAAA GGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT TCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAAAAAC GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAACAGAGA GGAAATAAGTGGAGTAAAATTGGAATCAATGGGAACTTACCAAATACTGT CAATTTATTCAACAGTGGCGAGTTCCCTAGCATTGGCAATCATGGTAGCT GGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT >MALLARD_VIETNAM_16_2003 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA AAGACACACAACGGGAAGCTCTGCGATCTAGATGGAGTGAAGCCTCTAAT TTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGAAACCCAATGTGTG ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT CCAGTCAATGACCTCTGTTACCCAGGGGATTTCAATGAATATGAAGAATT GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC CCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGGGTGAGCTCAGCA TGTCCATACCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTGT CAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA ACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG GCAGAGCAGACAAAGCTCTATCAAAATCCAACCACCTACATTTCCGTTGG GACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA AAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA CCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA ATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG ATAAACTCTAGTATGCCATTCCACAATATACACCCCCTCACCATCGGGGA ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGGCTCA GAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGATTATTTGGA GCTATAGCAGGTTTTATAGAGGGAGGATGGCAAGGAATGGTAGATGGTTG GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA CAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA GGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT TCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT CAATTTATTCTACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT GGTCTATCCTTATGGATGTGCTCCAATGGGTCGTTACAATGCAGA--- >CHICKEN_CK_160_2005 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA AAGACACACAACGGGAAGCTCTGTGATCTAGATGGAGTGAAGCCTCTAAT TTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTTGGAAACCCAATGTGTG ATGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAATGACTATGAAGAATT GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC CCAAAAGTTCTTGGTCCAGTCATGAAGCCTCATTAGGAGTGAGCTCAGCA TGTCCATATCAGGGAAAGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT CAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA ACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG GCAGAGCAGACAAAGCTCTATCAAAACCCAACCACCTACATTTCCGTTGG GACATCAACACTAAACCAGAGATTGGTACCAAGAATAGCTACTAGATCCA AAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA CCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA ATATGCATACAAAATTGTCAAGAAAGGGGACTCAACAATTATGAAAAGTG AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG ATAAACTCTAGTATGCCATTCCACAATATACACCCTCTCACCATCGGGGA ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA GAAATAGCCCTCAAAGAGAGAAAAGAAGAAAAAAGAGAGGATTATTTGGA GCTATAGCAGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGGTACGCTGCAGACA AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA CAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGGT TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA GGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT TCGAGTTCTATCATAAATGTGATAATGAATGTATGGAAAGTGTAAGGAAC GGAACGTATGACTACCCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAATTTACCAAATACTGT CAATTTATTCTACAGTAGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT GGTCTATCCTTATGGATGTGCTTCAATGGGTCGTTACAATGCAGAATT >CK_HK_WF157_2003 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA AAGACCCACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT TTTGAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTG ACGAATTCATCAATGTACCGGAATGGTCTTACATAGTGGAGAAGGCCAGT CCATCCAATGACCTCTGTTACCCAGGGGATTTCAACAATTATGAAGAACT GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC CCAAAAGCTCTTGGTCCAATCATGAAGCCTCATCAGGGGTGAGCTCAGCA TGTCCATACCTGGGAAAGCCCTCCTTTTTCAGAAATGTGGTATGGCTTAT CAAAAAGAACAGTACATACCCAACAATAAAGAGGAGCTACAATAATACCA ACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCATCCTAATGATGCG GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG AACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA AAGTAAACGGGCAAAGTGGAAGGATGGAGTTCTTCTGGACAATTTTAAAA CCGAATGATGCAATCAACTTCGAGAGTAATGGAAATTTCATTGCTCCAGA ATATGCATACAAAATTGTCAAGAAAGGGGACTCAGCAATTATGAAAAGTG AATTGGAATATGGTAACTGCAACACCAAGTGTCAAACTCCAATGGGGGCG ATAAACTCTAGTATGCCCTTCCACAACATACACCCTCTCACCATCGGGGA ATGCCCCAAATATGTGAAATCAAACAGACTAGTCCTTGCGACTGGGCTCA GAAATAGCCCTCAAAGAGAGAGAAGAAGAAAAAAGAGAGGACTATTTGGA GCTATAGCGGGTTTTATAGAGGGAGGATGGCAGGGAATGGTAGATGGTTG GTATGGATACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA AAGAATCCACTCAAAAGGCAATAGATGGAGTCACCAATAAGGTCAACTCG ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA TAACTTAGAAAGGAGAATAGAGAATTTAAACAAGAAGATGGAAGACGGAT TCCTAGATGTCTGGACTTATAATGCTGAACTTCTAGTTCTCATGGAAAAT GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA GGTCCGACTACAGCTTAGGGATAATGCAAAAGAGCTGGGTAACGGTTGTT TCGAGTTCTATCACAAATGTGATAATGAATGTATGGAAAGTGTAAGAAAC GGAACGTATGACTACTCGCAGTATTCAGAAGAAGCAAGACTAAAAAGAGA GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTAGCT GGTCTATCTTTATGGATGTGCTCCAATGGTTCGTTACAATGT------ >SWINE_ANHUI_1_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA TCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA AAGACACACAACGGGAAGCTCTGCGACCTAGATGGAGTGAAGCCTCTAAT TTTAAGAGATTGTAGTGTAGCTGGATGGCTCCTCGGGAACCCAATGTGTG ACGAATTCATCAATGTGCCGGAATGGTCTTACATAGTGGAGAAGGCCAAT CCAGCCAATGACCTCTGTTACCCAGGGGATTTCAACGACTATGAAGAACT GAAACACCTATTGAGCAGAATAAACCATTTTGAGAAAATTCAGATCATCC CCAAAAGTTCTTGGTCCGATCATGAAGCCTCATCAGGGGTGAGCTCAGCA TGTCCATACCAGGGAAGGTCCTCCTTTTTCAGAAATGTGGTATGGCTTAT CAAAAAGAACAGTGCATACCCAACAATAAAGAGGAGCTACAATAATACCA ACCAAGAAGATCTTTTGGTACTGTGGGGGATTCACCACCCTAATGATGCG GCAGAGCAGATAAAGCTCTATCAAAACCCAACCACCTATATTTCCGTTGG GACATCAACACTAAACCAGAGATTGGTACCAAAAATAGCTACTAGATCCA AAGTAAACGGACAAAGTGGAAGAATGGAGTTCTTCTGGACAATTTTAAAA CCGAATGATGCTATCAATTTCGAGAGTAATGGAAATTTCATTGCTCCAGA ATATGCATACAAAATTGTCAAGAAAGGGGACTCTGCAATTATGAAAAGTG AATTGGAATATGGCAACTGCAACACCAAGTGTCAAACTCCAGTGGGGGCG ATAAATTCTAGCATGCCATTCCACAACATACACCCTCTCACCATCGGGGA ATGCCCCAAATATGTGAAATCAAACAGATTAGTCCTTGCGACTGGACTCA GAAATGCCCCTCAAAGAGAGGGAAGAAGAAAAAAGAGAGGACTATTTGGA GCTATAGCAGGGTTTATAGAGGGAGGATGGCAGGGGATGGTAGATGGTTG GTATGGGTACCACCATAGCAATGAGCAGGGGAGTGGATACGCTGCAGACA AAGAATCCACTCAAAAAGCAATAGATGGAGTCACCAATAAGGTCAACTCG ATCATTGACAAAATGAACACTCAGTTTGAGGCCGTTGGAAGGGAATTTAA TAACTTAGAAAGGAGAATAGAAAATTTAAACAAGAAGATGGAGGACGGAT TCCTAGATGTCTGGACTTATAATGCTGAACTTCTGGTTCTCATGGAAAAT GAGAGAACTCTAGACTTTCATGACTCAAATGTCAAGAACCTTTACGACAA GGTCCGACTACAGCTTAGGGATAATGCAAAGGAGCTGGGTAACGGTTGTT TCGAGTTCTATCACAGATGTGATAATGAATGTATGGAAAGTGTAAGAAAC GGAACGTATGACTACCCGCAGTATTCGGAAGAAGCAAGACTAAACAGAGA GGAAATAAGTGGAGTAAAATTGGAATCAATAGGAACTTACCAAATACTGT CAATTTATTCAACAGTGGCGAGTTCCCTAGCACTGGCAATCATGGTGGCT GGTCTATCTTTATGGATGTGCTCCAATGGATCGTTACAATGCAGAATT \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/meme-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +((((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516):0.002095219592954275):0.003887237703073042)):0.003130608143291779,(CK_HK_WF157_2003:0.00663129750258774):0.004655295319725731):0.0116808817874948,(MALLARD_VIETNAM_16_2003:0.003244216605281072):0.0004125980823087554):0.0003400912533471183,CHICKEN_CK_160_2005:0.006168335080088849) diff -r 000000000000 -r 7c86ceaf523c test-data/meme-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,2535 @@ +{ + "MLE":{ + "content":{ + "0": [ +[0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 0, 3.477431520841965, 1, 0, 0.6666666666666666, 0, 0.1244820193331403], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 0, 3.741010141509965, 1, 0, 0.6666666666666666, 0, 0.1339173737771157], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 0, 3.515256679835982, 1, 0, 0.6666666666666666, 0, 0.1258360509351867], + [0, 0, 0, 2.551430028273134, 1, 0, 0.6666666666666666, 0, 0.09133383654087057], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 0.09433309141367374, 3.23711069521408, 0.9056669085863263, 0.5595133528189606, 0.4135250593893275, 0, 0.1049479822225346], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 1, 0, 0, 0, 1, 0, 0], + [0, 0, 0, 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the proportion of the tree evolving neutrally or under negative selection"], + ["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"], + ["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"], + ["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"], + ["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond, Steven Weaver", + "citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.", + "contact":"spond@temple.edu", + "info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.1.1" + }, + "branch attributes":{ + "0":{ + "CHICKEN_CK_160_2005":{ + "EBF site 100 (partition 1)":1, + "EBF site 102 (partition 1)":0.4618577742407079, + "EBF site 104 (partition 1)":1, + "EBF site 11 (partition 1)":1, + "EBF site 112 (partition 1)":1, + "EBF site 113 (partition 1)":1, + "EBF site 117 (partition 1)":1, + "EBF site 12 (partition 1)":1, + "EBF site 136 (partition 1)":1, + "EBF site 140 (partition 1)":1, + "EBF site 142 (partition 1)":1, + "EBF site 145 (partition 1)":1, + "EBF site 146 (partition 1)":1, + "EBF site 152 (partition 1)":1, + "EBF site 153 (partition 1)":1, + "EBF site 154 (partition 1)":1, + "EBF site 155 (partition 1)":1, + "EBF site 156 (partition 1)":1, + "EBF site 157 (partition 1)":1, + "EBF site 16 (partition 1)":0.8956232595692452, + "EBF site 167 (partition 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site 527 (partition 1)":{ + "attribute type":"branch label", + "display order":529 + }, + "EBF site 529 (partition 1)":{ + "attribute type":"branch label", + "display order":531 + }, + "EBF site 537 (partition 1)":{ + "attribute type":"branch label", + "display order":539 + }, + "EBF site 539 (partition 1)":{ + "attribute type":"branch label", + "display order":541 + }, + "EBF site 545 (partition 1)":{ + "attribute type":"branch label", + "display order":547 + }, + "EBF site 549 (partition 1)":{ + "attribute type":"branch label", + "display order":551 + }, + "EBF site 553 (partition 1)":{ + "attribute type":"branch label", + "display order":555 + }, + "EBF site 558 (partition 1)":{ + "attribute type":"branch label", + "display order":560 + }, + "EBF site 560 (partition 1)":{ + "attribute type":"branch label", + "display order":562 + }, + "EBF site 564 (partition 1)":{ + "attribute type":"branch label", + "display order":566 + }, + "EBF site 58 (partition 1)":{ + "attribute 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"attribute type":"branch length", + "display order":1 + }, + "Nucleotide GTR":{ + "attribute type":"branch length", + "display order":0 + }, + "original name":{ + "attribute type":"node label", + "display order":-1 + } + } + }, + "data partitions":{ + "0":{ + "coverage": [ +[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 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+ "name":"meme.filter.default" + } + }, + "fits":{ + "Global MG94xREV":{ + "AIC-c":6011.13695012892, + "Equilibrium frequencies": [ +[0.0487448731499957], + [0.02916309663834602], + [0.03100171502919514], + [0.03392179881163448], + [0.02040080210426937], + [0.01220539771302355], + [0.01297489997065711], + [0.01419701929364967], + [0.02306796533539959], + [0.0138011088931582], + [0.01467121445635504], + [0.01605311140503505], + [0.03067687144383888], + [0.01835336741416609], + [0.01951047494908151], + [0.02134818687672324], + [0.02126077850204813], + [0.01271990463804815], + [0.01352184453103644], + [0.01479548113102975], + [0.008898103672735205], + [0.005323560008197935], + [0.005659189501089015], + [0.006192234446128948], + [0.010061425331433], + [0.006019552422614294], + [0.006399061496227086], + [0.007001795754005012], + [0.01338015932252603], + [0.008005085543223482], + [0.008509774660521757], + [0.009311319186526256], + [0.04013232935583105], + [0.02401038147590574], + 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[0.184883858035609], + [0.2307510906732697], + [0.2365287112368824] + ], + "Log Likelihood":-3056.215005465311, + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.1810796022573985, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.08708610799393901, + "Substitution rate from nucleotide C to nucleotide G":0.02931879134098465, + "Substitution rate from nucleotide C to nucleotide T":1.419136867291551, + "Substitution rate from nucleotide G to nucleotide T":0.1065442350926398 + }, + "display order":0, + "estimated parameters":20 + } + }, + "input":{ + "file name":"/tmp/tmpdqyv1aux/job_working_directory/000/3/working/./meme_input.fa", + "number of sequences":5, + "number of sites":566, + "partition count":1, + "trees":{ + 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+ "rawsites": 1698 + } + ], + "created": "2014-10-21T20:03:25.798Z" + }, + "status_stack": [ + "In Queue", + "Running", + "Completed" + ], + "type": "relax" +} diff -r 000000000000 -r 7c86ceaf523c test-data/prime-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +>HUMAN_VIETNAM_CL105_2005 ATGGAGAAAATAGTGCTTCTTTTTGCGATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_HEBEI_326_2005 ATGGAGAGAATAGTGCTTCTTCTTGCAATAATCGGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAG >CHICKEN_HONGKONG_915_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HUMAN_VIETNAM_3062_2004 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_HONGKONG_W355_97 ATGGAGAAAATAGTGCTTCTTCTTGCAACAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >MALLARD_VIETNAM_16_2003 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CHICKEN_CK_160_2005 ATGGAGAAAATAGTGCTTCTTTTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCAACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >CK_HK_WF157_2003 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >SWINE_ANHUI_1_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAGGTGA TCAGATTTGCACTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCTCAAGACATACTGGAA >HONGKONG_1_97_98 ------------------------------------------------GA CCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGATA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >GOOSE_SHANTOU_2216_2005 ATGGAGAAAATAGTGCTTCTTCTTGCAATAATCAGCCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAACGTTACTGTTACACATGCCCAAGACATACTGGAA >PEREGRINEFALCON_HK_D0028_2004 ATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAGTCTTGTTAAAAGTGA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA >HONGKONG_1_538_97 ------------------------------------------------GA TCAGATTTGCATTGGTTACCATGCAAACAACTCGACAGAGCAGGTTGACA CAATAATGGAAAAGAATGTTACTGTTACACATGCCCAAGACATACTGGAA \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/prime-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prime-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ 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independent non-synonymous rate a site"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"], + ["PRIME LogL", "Site Log-likelihood under the PRIME model"], + ["FEL LogL", "Site Log-likelihood under the FEL model"], + ["p-value", "Omnibus p-value (any property is important)"], + ["λ1", "Importance for Factor I bipolar"], + ["p1", "p-value for non-zero effect of Factor I bipolar"], + ["LogL1", "Log likelihood when there is no effect of Factor I bipolar"], + ["λ2", "Importance for Factor II secondary structure"], + ["p2", "p-value for non-zero effect of Factor II secondary structure"], + ["LogL2", "Log likelihood when there is no effect of Factor II secondary structure"], + ["λ3", "Importance for Factor III volume"], + ["p3", "p-value for non-zero effect of Factor III volume"], + ["LogL3", "Log likelihood when there is no effect of Factor III volume"], + ["λ4", "Importance for Factor IV composition"], + ["p4", "p-value for non-zero effect of Factor IV composition"], + ["LogL4", "Log likelihood when there is no effect of Factor IV composition"], + ["λ5", "Importance for Factor V charge"], + ["p5", "p-value for non-zero effect of Factor V charge"], + ["LogL5", "Log likelihood when there is no effect of Factor V charge"] + ] + }, + "analysis":{ + "authors":"Sergei L. Kosakovsky Pond", + "citation":"TBD", + "contact":"spond@temple.edu", + "info":"PRIME (PRoperty Informed Model of Evolution). Given a set of N amino-acid properties,\n fit a site-level model where non-synonymous rates depend on how much a non-synonymous substitution changes the \n properties of the residue, beta (X,Y) = Exp (log_omega - lambda_1 * diff_1 (X,Y )- lambda_2 * diff_2 (X,Y) -...).\n When lambda_k > 0, changes in property k are disfavored and when lambda_k < 0 -- they are promoted.\n At each site, N tests are performed\n A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"0.0.1" + }, + "branch attributes":{ + "0":{ + "CHICKEN_CK_160_2005":{ + "Global MG94xREV":0.006875905528136641, + "Nucleotide GTR":0.006740765844759078, + "original name":"CHICKEN_CK_160_2005" + }, + "CHICKEN_HEBEI_326_2005":{ + "Global MG94xREV":0.03000509055831138, + "Nucleotide GTR":0.02817726192677478, + "original name":"CHICKEN_HEBEI_326_2005" + }, + "CHICKEN_HONGKONG_915_97":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"CHICKEN_HONGKONG_915_97" + }, + "CK_HK_WF157_2003":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"CK_HK_WF157_2003" + }, + "GOOSE_HONGKONG_W355_97":{ + "Global MG94xREV":0, + "Nucleotide GTR":0, + "original name":"GOOSE_HONGKONG_W355_97" + }, + "GOOSE_SHANTOU_2216_2005":{ + "Global MG94xREV":0.008912012248907763, + "Nucleotide 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nucleotide A to nucleotide C":0, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0, + "Substitution rate from nucleotide C to nucleotide G":0, + "Substitution rate from nucleotide C to nucleotide T":1.816257034982832, + "Substitution rate from nucleotide G to nucleotide T":0 + }, + "display order":0, + "estimated parameters":36 + } + }, + "input":{ + "file name":"/Users/sergei/Development/tools-iuc/tools/hyphy/test-data/prime-in1.fa", + "number of sequences":13, + "number of sites":50, + "partition count":1, + "trees":{ + "0":"(((((CHICKEN_HEBEI_326_2005:0.02100885319673648,(SWINE_ANHUI_1_2004:0.007702393698306516)Node7:0.002095219592954275)Node5:0.003887237703073042)Node4:0.003404921392531202,(((CHICKEN_HONGKONG_915_97:-1,(GOOSE_HONGKONG_W355_97:-1)Node13:0.002899766890966483)Node11:0.001306376767766534,HONGKONG_1_97_98:0.003844928589233716)Node10:0.000182535836694054,HONGKONG_1_538_97:-1)Node9:0.02096173714686362)Node3:0.003130608143291779,(((GOOSE_SHANTOU_2216_2005:0.006207842095177651)Node19:0.002530613798219486,PEREGRINEFALCON_HK_D0028_2004:0.003608296348267232)Node18:0.003288900909856382,CK_HK_WF157_2003:0.00663129750258774)Node17:0.004655295319725731)Node2:0.0116808817874948,(((HUMAN_VIETNAM_CL105_2005:0.006521522005742001)Node25:0.001967887030302483,HUMAN_VIETNAM_3062_2004:0.001641397323851184)Node24:0.0003125512332168847,MALLARD_VIETNAM_16_2003:0.003244216605281072)Node23:0.0004125980823087554,CHICKEN_CK_160_2005:0.006168335080088849)" + } + }, + "tested":{ + "0":{ + "CHICKEN_CK_160_2005":"test", + "CHICKEN_HEBEI_326_2005":"test", + "CHICKEN_HONGKONG_915_97":"test", + "CK_HK_WF157_2003":"test", + "GOOSE_HONGKONG_W355_97":"test", + "GOOSE_SHANTOU_2216_2005":"test", + "HONGKONG_1_538_97":"test", + "HONGKONG_1_97_98":"test", + "HUMAN_VIETNAM_3062_2004":"test", + "HUMAN_VIETNAM_CL105_2005":"test", + "MALLARD_VIETNAM_16_2003":"test", + "Node10":"test", + "Node11":"test", + "Node13":"test", + "Node17":"test", + "Node18":"test", + "Node19":"test", + "Node2":"test", + "Node23":"test", + "Node24":"test", + "Node25":"test", + "Node3":"test", + "Node4":"test", + "Node5":"test", + "Node7":"test", + "Node9":"test", + "PEREGRINEFALCON_HK_D0028_2004":"test", + "SWINE_ANHUI_1_2004":"test" + } + }, + "timers":{ + "Model fitting":{ + "order":1, + "timer":3 + }, + "PRIME analysis":{ + "order":2, + "timer":86 + }, + "Total time":{ + "order":0, + "timer":89 + } + } +} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/relax-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,20 @@ +>Human +AAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Chimp +GAAGAGATTACGAATGCCTTGGAAACCTGGGGTGCCTTGGGTCAGGACATCAACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGACGATATAAAATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAAGAGACTTTCAAGGAAAAAGATACATATAAGCTATTTAAAAATGGAACTCTGAAAATTAAGCAT---CTGAAGACCGATGATCAGGATATCTACAAGGTATCAATATATGATACAAAAGGAAAAAATGTGTTGGAAAAAATATTTGATTTGAAGATTCAAGAGAGGGTCTCAAAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAGGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCAAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGTGTCGAGCCTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Baboon +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAAATGGGAGAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAATTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGACCCCGAATTAAACCTGTATCAAGATGGGAAACATCTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>RhMonkey +AAAGAGATTAGGAATGCTTTGGAAACCTGGGGAGCGCTGGGTCAGGACATCGACTTGGACATTCCTAGTTTTCAAATGAGTGATGATATTGATGATATAAGATGGGAAAAAACTTCAGACAAGAAAAAGATTGCACAATTCAGAAAAGAGAAGGAGACTTTCGAGGAAAAAGATGCATATAAGCTATTTAAAAACGGAACTCTGAAAAYTAAGCAT---CTGAAGATCCATGATCAGGATAGCTACAAGGTATCAATATACGATACAAAAGGAAAAAATGTGTTGGAAAAAACATTTGATTTGAAGATTCAAGAGAGGGTCTCAGAACCAAAGATCTCCTGGACTTGTATCAACACAACCCTGACCTGTGAAGTAATGAATGGAACTGRCCCCGAATTAAACCTGTATCAAGATGGGAAACATGTAAAA---CTTTCTCAGAGGGTCATCACACACAAGTGGACCACCAGCCTGAGTGCGAAATTCAAGTGCACAGCAGGGAACAAAGTCAGCAAGGAATCCAGGATGGAGACTGTCAGCTGTCCAGAGAAAGGTCTGGAC +>Cow +------------GAAAGCATTGTCGTCTGGGGTGCCCTGGATCATGACCTCAACCTGGACATTCCTGGTTTTCCAAGAAGTGATATAGTGGCAGATATAAAATGGAACAGA------AACAAAAACAAGATTGCACGAATAAAGAAAGATATGCCACTTCACAATGAAATGGACAAATATGATATGTTTACAAATGGAACTCTGAAAATTAAAACT---CTGATGAGAAACGATAGTGGTCTCTATGAGGTAGAGGTTTATGATTCAAATGGAGTAAACCTACTGAGCAAAAAATTTGATTTGAAGATTCAAGAGATGCTCTCAGGACCTGAAATTAACTGGATCTGTACCAACAGAACTGTGAGCTGCAAGGTAGAAAATGGAAGTAATCCTAAATTACAACTGTTTTTAAATACGACCCGTGTCAAACAAGATCATGGGAAGCTCATCACCTACACGTGGAACACCAGATGGAATAAAACATTCAAGTGCGTGGCGAGTAACCATGTCGATAGCAAAGTCAGCATAGAGATCGCCGTGTGTCCAGATGAAGGTCTGGAT +>Pig +---------------ACTGAGGTTGTCTGGGGCATCGTGGATCAAGACATCAACCTGGACATTCCTGAACTTTCAAAACATGATAACGTAGATCATATACGATGGCAGAAG------AATGAAAACAAGATCGCAGAATTTAAAAAAAACAAAGAAACTCACCCTGTGAAAGACACATACATGATGTTACCAAATGGAACTCTGAGAATTAAAGAT---CTGAAGAGAGATGATGAGGGTATCTACAAGGTAACTGTCTATGCTACGGATGGAAAACACATGCTGGAGAGAAAATTTGATTTGCCGATTCTAGATGGGGTCTCAAAACCTGTAATCTCCTGGAGCTGTGCCGACAAAACGGTGACCTGTGAGGTAGCAGAAGGAAGTGACCCTAAGTTAAAACTGTATGTAAATAAGTCCACTGCCAGAGAAGGTCGTCAGAAGGTCATCCTGTGGAAGTGGAACACCAAATGGAGCACATTATTCAAGTGTGTGGCCAGTAACAACGCCAGTGAGCAAATCAGCATGGTGACCATCAGTTGTACGGGGCAAGGTCTGGAT +>Horse +------------AAGAATATCACCATCTTGGGTGCCCTGGAACGTGATATCAACCTGGACATTCCTGCTTTTCAAATGAGTGAGCATGTAGAAGATATACAATGGAGCAAA------GGAAAAACCAAGATTGCAAAATTCAAAAATGGCAGTATGACTTTCCAGAAAGATAAAACATACGAGGTATTAAAAAATGGAACTCTGAAAATTAAACAT---CTGGAGAGAATTCATGAAGGTACCTACAAGGTAGACGCATATGATAGTGATGGAAAAAATGTGTTGGAGGAAACATTTCATTTGAGCCTTCTAGAGATGGTCTCAAAACCTAATATCTCCTGGAGCTGCACCAACACCACCCTGACCTGCGAGGTGACAAAAGGAACTGACTTTGAGTTAAAACTCTATCTAAATGGGAGAATGATCCAAAAAAGTCCTCGCAAAGTCATCGTATACAAGCGGGCCAGCAACCAAATTGCGTCCTTCAAGTGCACAGCCAATAACACAGTCAGCGAGGAAAGCAGCTCTGTGGTCATCAGGTGTACAGAGAAAGGTCTGGAT +>Cat +---------GCAAATGATGATATCGTCTGGGGTACCCTGGGTCAGGACATCAACCTGGACATTCCTGATTCTCAA---GGGATTAATATAGATGATATACACTGGGAAAAA------GGCAAGAAGAAGGTGGCGAGGTTCCAAATTAGCAACAAGCCTAAGAATCCAGATGAAAAATATAATGTGTCAATGAATGGAACTCTGAAAATTAAACAT---CTGATGCTAGAAGACTGCGATACCTACAAGGTTGTTATATACGATAAGGATGGAAAGAATGTGTTGGATAAAACATTTCAGCTGAAGATTCAAGAGAAGGTCTCAACGCCTAACATCGACTGGAATTGTATCAACAAAACCCTGGTCTGTAAGGTATCAAATGGAACAGACCCTGAATTAAAACTGTACGTAAATGGGACCAGTATCAAGCCCGTTTCTTCGAAGTTCAGCACATACAGGTTTATAAACAAGCAGAAGATATTAGTCAACTGCACGGCAGAAAACAAAGTCAGCAAGGAAAGCGACGTGAAGATGATCACTTGTTCAGAGAAGGGTCTGGAC +>Mouse +---------AGAGACAATGAGACCATCTGGGGTGTCTTGGGTCATGGCATCACCCTGAACATCCCCAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGTAAGG------AGGGGCACCCTGGTCGCAGAGTTTAAAAGGAAGAAGCCACCTTTTTTGATATCAGAAACGTATGAGGTCTTAGCAAACGGATCCCTGAAGATAAAGAAGCCGATGATGAGAAACGACAGTGGCACCTATAATGTAATGGTGTATGGCACAAATGGGATGACTAGGCTGGAGAAGGACCTGGACGTGAGGATTCTGGAGAGGGTCTCAAAGCCCATGATCCACTGGGAATGCCCCAACACAACCCTGACCTGTGCGGTCTTGCAAGGGACAGATTTTGAACTGAAGCTGTATCAAGGGGAAACACTACTCAATAGTCTCCCCCAGAAGAACATGAGTTACCAGTGG---ACCAACCTGAACGCACCATTCAAGTGTGAGGCGATAAACCCGGTCAGCAAGGAGTCTAAGATGGAAGTTGTTAACTGTCCAGAGAAAGGTCTGTCC +>Rat +---------AGAGACAGTGGGACCGTCTGGGGTGCCCTGGGTCATGGCATCAACCTGAACATCCCTAACTTTCAAATGACTGATGATATTGATGAGGTGCGATGGGAGAGG------GGGAGCACCCTGGTTGCCGAGTTTAAAAGGAAGATGAAGCCTTTTTTGAAATCGGGAGCATTTGAGATCTTAGCAAATGGAGACTTGAAGATAAAGAAT---CTGACAAGAGATGACAGTGGCACCTATAATGTAACGGTATACAGCACAAATGGGACACGTATCCTGGACAAGGCACTGGACTTGAGGATTCTAGAGATGGTCTCAAAGCCGATGATCTACTGGGAGTGCAGCAACGCAACCCTGACCTGTGAGGTCTTGGAAGGAACAGATGTTGAACTAAAGCTGTACCAAGGAAAGGAGCATCTCAGGAGCCTCCGTCAGAAGACCATGAGTTACCAGTGG---ACCAACCTGAGAGCACCGTTTAAGTGCAAGGCGGTAAACAGGGTCAGCCAGGAGTCTGAGATGGAAGTTGTCAACTGTCCAGAGAAAGGTCTGCCC diff -r 000000000000 -r 7c86ceaf523c test-data/relax-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +((((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Horse{TEST}:0.165787,Cat{TEST}:0.264806):0.058611,((RhMonkey:0.002015,Baboon:0.003108):0.022733,(Human:0.004349,Chimp:0.000799):0.011873):0.101856):0.340802,Rat:0.050958,Mouse:0.09795) \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/relax-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-in2.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,1 @@ +((((Pig{TEST}:0.147969,Cow{TEST}:0.21343){TEST}:0.085099,Horse:0.165787,Cat:0.264806){TEST}:0.058611,((RhMonkey{REFERENCE}:0.002015,Baboon{REFERENCE}:0.003108){REFERENCE}:0.022733,(Human{REFERENCE}:0.004349,Chimp{REFERENCE}:0.000799):0.011873){REFERENCE}:0.101856){REFERENCE}:0.340802,Rat{REFERENCE}:0.050958,Mouse{REFERENCE}:0.09795) diff -r 000000000000 -r 7c86ceaf523c test-data/relax-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/relax-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,499 @@ +{ + "analysis":{ + "info":"RELAX (a random effects test of selection relaxation) uses a random effects branch-site model framework to test whether a set of 'Test' branches evolves under relaxed selection relative to a set of 'Reference' branches (R), as measured by the relaxation parameter (K).\n Version 2.1 adds a check for stability in K estimates to try to mitigate convergence problems", + "version":"2.1", + "citation":"RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015). Mol Biol Evol 32 (3): 820-832", + "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group", + "contact":"spond@temple.edu", + "requirements":"in-frame codon alignment and a phylogenetic tree, with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)" + }, + "input":{ + "file name":"/home/galaxystaging/galaxy/database/jobs_directory/000/79/working/relax_input.fa", + "number of sequences":10, + "number of sites":187, + "partition count":1, + "trees":{ + "0":"((((Pig:0.147969,Cow:0.21343)Node3:0.085099,Horse:0.165787,Cat:0.264806)Node2:0.058611,((RhMonkey:0.002015,Baboon:0.003108)Node9:0.022733,(Human:0.004349,Chimp:0.000799)Node12:0.011873)Node8:0.101856)Node1:0.340802,Rat:0.050958,Mouse:0.09795)" + } + }, + "fits":{ + "Nucleotide GTR":{ + "Log Likelihood":-3531.964032193222, + "estimated parameters":24, + "AIC-c":7112.142925621896, + "Equilibrium frequencies":[ + [0.3563279857397504], + [0.1837789661319073], + [0.2402852049910873], + [0.2196078431372549] + ], + "Rate Distributions":{ + "Substitution rate from nucleotide A to nucleotide C":0.5465757107930838, + "Substitution rate from nucleotide A to nucleotide G":1, + "Substitution rate from nucleotide A to nucleotide T":0.264131123736109, + "Substitution rate from nucleotide C to nucleotide G":0.4861812992450388, + "Substitution rate from nucleotide C to nucleotide T":1.017887589835735, + "Substitution rate from nucleotide G to nucleotide T":0.3021773696987065 + }, + "display order":0 + }, + "MG94xREV with separate rates for branch sets":{ + "Log Likelihood":-3460.931903299487, + "estimated parameters":32, + "AIC-c":6987.013507197776, + "Equilibrium frequencies":[ + [0.04785168648208005], + [0.03911346079312019], + [0.04842054060317301], + [0.04069665666515385], + [0.01817010744778396], + [0.01485205303123071], + [0.01838611113045968], + [0.01545321970309948], + [0.0190138898893362], + [0.01554175184587827], + [0.01923992433904378], + [0.01617083546230154], + [0.02796925133965702], + [0.02286176927319543], + [0.02830174586718859], + [0.02378714529482007], + [0.01687870337957799], + [0.01379647304851128], + [0.01707935503225849], + [0.01435491300079667], + [0.006409133648843443], + [0.005238757839512795], + [0.006485324528555602], + [0.005450807083377185], + [0.006706760641638982], + [0.005482034985409045], + [0.006786489669196017], + [0.005703931360295163], + [0.009865581170012171], + [0.008064021368173151], + [0.009982861811889655], + [0.008390428826966174], + [0.03287895020631181], + [0.02687490503171972], + [0.033269810543681], + [0.0279627207822247], + [0.01248470225271473], + [0.01020486315060615], + [0.01263311863778268], + [0.01061792547971484], + [0.01306446616325414], + [0.01067875601941112], + [0.01321977470017749], + [0.01111100011404158], + [0.01921770557551369], + [0.01570834862514353], + [0.01944616295744266], + [0.01634417558076203], + [0.01975257768318274], + [0.02055210293142003], + [0.009176034326710849], + [0.007500393094996483], + [0.00928511773266342], + [0.007803986567571961], + [0.00784869593340758], + [0.009716299514778986], + [0.008166387662818644], + [0.01412467213650941], + [0.01154535713247913], + [0.01429258425298098], + [0.01201267864744234] + ], + "Rate Distributions":{ + "non-synonymous/synonymous rate ratio for *Reference*":[ + [1.617765969026557, 1] + ], + "non-synonymous/synonymous rate ratio for *Test*":[ + [0.7687683974183303, 1] + ] + }, + "display order":1 + }, + "General descriptive":{ + "Log Likelihood":-3420.975369746331, + "estimated parameters":51, + "AIC-c":6946.868231241836, + "Rate Distributions":{ + "Shared":{ + "0":{ + "omega":1e-08, + "proportion":0.2345034364701236 + }, + "1":{ + "omega":1e-08, + "proportion":0.3180344596999608 + }, + "2":{ + "omega":6.64943557055033, + "proportion":0.4474621038299156 + } + } + }, + "display order":4 + }, + "RELAX alternative":{ + "Log Likelihood":-3429.125323833579, + "estimated parameters":36, + "AIC-c":6931.704002822642, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0, + "proportion":0.1993913071931658 + }, + "1":{ + "omega":0, + "proportion":0.3360341729181165 + }, + "2":{ + "omega":2.153056268947235, + "proportion":0.4645745198887177 + } + }, + "Reference":{ + "0":{ + "omega":0, + "proportion":0.1993913071931658 + }, + "1":{ + "omega":0, + "proportion":0.3360341729181165 + }, + "2":{ + "omega":6.166712663934246, + "proportion":0.4645745198887177 + } + } + }, + "display order":2 + }, + "RELAX null":{ + "Log Likelihood":-3437.187429488768, + "estimated parameters":35, + "AIC-c":6945.748904779063, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0.1177689533662908, + "proportion":0.4926494715348529 + }, + "1":{ + "omega":0.3195682613972807, + "proportion":0.1517366025099117 + }, + "2":{ + "omega":3.893733071412322, + "proportion":0.3556139259552353 + } + }, + "Reference":{ + "0":{ + "omega":0.1177689533662908, + "proportion":0.4926494715348529 + }, + "1":{ + "omega":0.3195682613972807, + "proportion":0.1517366025099117 + }, + "2":{ + "omega":3.893733071412322, + "proportion":0.3556139259552353 + } + } + }, + "display order":3 + }, + "RELAX partitioned descriptive":{ + "Log Likelihood":-3427.515821600644, + "estimated parameters":40, + "AIC-c":6936.824972889643, + "Rate Distributions":{ + "Test":{ + "0":{ + "omega":0.2264899618249929, + "proportion":0.1370778077745601 + }, + "1":{ + "omega":0.2328054750512875, + "proportion":0.6322930022247097 + }, + "2":{ + "omega":4.13407071706127, + "proportion":0.2306291900007301 + } + }, + "Reference":{ + "0":{ + "omega":0, + "proportion":0.09054841512283768 + }, + "1":{ + "omega":0, + "proportion":0.4231976237742962 + }, + "2":{ + "omega":5.975493863572218, + "proportion":0.4862539611028661 + } + } + }, + "display order":5 + } + }, + "timers":{ + "Overall":{ + "timer":562, + "order":0 + }, + "Preliminary model fitting":{ + 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1.725289655759397], + [1.416174943672039, 1.583825056327962, 0, 0, 0.4720583145573461, 0, 0, 0, 1, 1, 1.725289655759397], + [0.566048512190645, 2.433951487809356, 2, 3, 0.1886828373968816, 3.533266066295039, 1.232563596696871, -1.333516642795554, 0.9504034442939914, 0.2397204872545077, 1.725289655759397] + ] + } + } + }, + "headers": [ +["ES", "Expected synonymous sites"], + ["EN", "Expected non-synonymous sites"], + ["S", "Inferred synonymous substitutions"], + ["N", "Inferred non-synonymous substitutions"], + ["P[S]", "Expected proportion of synonymous sites"], + ["dS", "Inferred synonymous susbsitution rate"], + ["dN", "Inferred non-synonymous susbsitution rate"], + ["dN-dS", "Scaled by the length of the tested branches"], + ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with Ps probability of success"], + ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with Ps probability of success"], + ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"] + ] + }, + "analysis":{ + "authors":"Sergei L Kosakovsky Pond and Simon DW Frost", + "citation":"Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection (2005). _Mol Biol Evol_ 22 (5): 1208-1222", + "contact":"spond@temple.edu", + "info":"SLAC (Single Likelihood Ancestor Counting)\n uses a maximum likelihood ancestral state reconstruction\n and minimum path substitution counting to estimate site - level\n dS and dN,\n and applies a simple binomial - based test to test\n if dS differs drom dN.\n The estimates aggregate information over all branches,\n so the signal is derived from\n pervasive diversification or conservation. A subset of branches can be selected\n for testing as well.\n Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ", + "requirements":"in-frame codon alignment and a phylogenetic tree", + "version":"2.00" + }, + "branch attributes":{ + "0":{ + "Baboon":{ + "Global MG94xREV":0.001710698008755675, + "Nucleotide GTR":0.001679501710016974, + "amino-acid": [ +["K", "E", "I", "R", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "D", "L", "D", "I", "P", "S", "F", "Q", "M", "S", "D", "D", "I", "D", "D", "I", "K", "W", "E", "K", "T", "S", "D", "K", "K", "K", "I", "A", "Q", "F", "R", "K", "E", "K", "E", "T", "F", "E", "E", "K", "D", "A", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "I", "H", "D", "Q", "D", "S", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "T", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "E", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", 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GTR":0.2660443541848668, + "amino-acid": [ +["-", "-", "-", "A", "N", "D", "D", "I", "V", "W", "G", "T", "L", "G", "Q", "D", "I", "N", "L", "D", "I", "P", "D", "S", "Q", "-", "G", "I", "N", "I", "D", "D", "I", "H", "W", "E", "K", "-", "-", "G", "K", "K", "K", "V", "A", "R", "F", "Q", "I", "S", "N", "K", "P", "K", "N", "P", "D", "E", "K", "Y", "N", "V", "S", "M", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "M", "L", "E", "D", "C", "D", "T", "Y", "K", "V", "V", "I", "Y", "D", "K", "D", "G", "K", "N", "V", "L", "D", "K", "T", "F", "Q", "L", "K", "I", "Q", "E", "K", "V", "S", "T", "P", "N", "I", "D", "W", "N", "C", "I", "N", "K", "T", "L", "V", "C", "K", "V", "S", "N", "G", "T", "D", "P", "E", "L", "K", "L", "Y", "V", "N", "G", "T", "S", "I", "K", "P", "V", "S", "S", "K", "F", "S", "T", "Y", "R", "F", "I", "N", "K", "Q", "K", "I", "L", "V", "N", "C", "T", "A", "E", "N", "K", "V", "S", "K", "E", "S", "D", "V", "K", "M", "I", "T", "C", "S", "E", "K", "G", "L", "D"] + ], + "codon": [ 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[0.6412303110713271, 2.204540734106206, 2, 4, 0.2253274423316525, 3.11900414791454, 1.814436874817708, -0.7561439140041785, 0.8675922736594839, 0.4066864498982908, 1.725289655759397], + [0.6193320811838234, 2.216614432620847, 1.833333333333333, 6.583333333333334, 0.2223646822781374, 2.896430383501774, 2.963446495360119, 0.2214729670897475, 0.6239037738276377, 0.682079854204686, 1.717881683785966], + [0.9361680866134802, 2.06383191338652, 1, 5, 0.31205602887116, 1.068184244153662, 2.429153900387575, 0.7924529737466629, 0.390668869851127, 0.8956812645675155, 1.725289655759397], + [0.9653607734842997, 2.034639226515701, 1, 5, 0.3217869244947665, 1.035882156668409, 2.457438122119787, 0.8239520597054015, 0.3743639219220316, 0.9026811539630719, 1.725289655759397], + [0.7802855479936737, 1.899691410376977, 0.5, 5.5, 0.2911538271090454, 0.6407910556406382, 2.895207068872609, 1.306688419365544, 0.2831724012199115, 0.8731437136526612, 1.725289655759397], + [0.7066525864062013, 2.15681049336373, 1, 1, 0.2467825031161143, 1.415122535793247, 0.4636475958721875, -0.5514870716026298, 0.9390983961557451, 0.4326634023879736, 1.725289655759397], + [0.9278486054607593, 2.072151394539241, 0, 5, 0.3092828684869197, 0, 2.412951106360541, 1.398577391515435, 0.157217591444011, 1, 1.725289655759397], + [0.6038215671871429, 2.396178432812857, 0, 2, 0.2012738557290476, 0, 0.8346623826557915, 0.4837810160569296, 0.6379634535419422, 1, 1.725289655759397], + [0.9068301121228288, 2.089207511015492, 2.333333333333333, 5.666666666666667, 0.3026764767970213, 2.573065563373448, 2.712352237290347, 0.08073234164010072, 0.63032116147405, 0.6516441553548806, 1.725289655759397], + [0.4008436757486826, 2.029330170444659, 0, 3, 0.1649444447674268, 0, 1.478320306716108, 0.8568533995327389, 0.5822990862226557, 1, 1.725289655759397], + [0.7389643787939167, 2.086005205876958, 0, 3, 0.2615831274091435, 0, 1.438155567180762, 0.8335734016487505, 0.4026287982935924, 1, 1.725289655759397], + [0.1576624310073349, 1.666259984674887, 0, 3, 0.0864414131060299, 0, 1.800439323750157, 1.043557710868951, 0.7624462139510615, 1, 1.725289655759397], + [0.7706672565854851, 2.229332743414515, 1, 4, 0.256889085528495, 1.312960703174895, 1.758629750260521, 0.1849831169945381, 0.6761938496473037, 0.7109049246297867, 1.537146090755571], + [0.918128613830821, 2.08187138616918, 0, 2, 0.3060428712769402, 0, 0.960674138319452, 0.5568190449137106, 0.4815764965055533, 1, 1.725289655759397], + [0.5100975226897894, 2.436862688713398, 0, 4, 0.1730927756391077, 0, 1.64145481751042, 0.9514082531190525, 0.4675490133082674, 1, 1.725289655759397], + [0.8966968578847343, 1.642037753317381, 1, 4, 0.3538344523852633, 1.115204086204733, 2.442702979734417, 0.7694353751546591, 0.4210688108565674, 0.887353165393325, 1.725289655759397], + [0.5446996599261835, 2.444824668946187, 2, 6, 0.1822027854617396, 3.671748207573758, 2.469395198364968, -0.6395677508663903, 0.824295415527497, 0.458673880911332, 1.725289655759397], + [0.9393647524582979, 2.050382206902235, 2, 4, 0.3141954035666, 2.129098409074901, 1.95123259106649, -0.103093308079983, 0.7175136294201356, 0.6100548468646573, 1.725289655759397], + [0.9930261789614826, 1.729576569823436, 2, 6, 0.3647341425056095, 2.014045593532712, 3.604897778287483, 0.8433433604945434, 0.3931728711383731, 0.8516454740288871, 1.725289655759397], + [0.4642011124998626, 2.535798887500138, 1, 1, 0.1547337041666208, 2.154238697565155, 0.3943530399549264, -1.020052286139514, 0.9760574807948768, 0.2855248891281182, 1.725289655759397], + [0.6749720260888831, 2.190994286795494, 0, 1, 0.235512895966169, 0, 0.4564137871224579, 0.2645432815289004, 0.764487104033831, 1, 1.725289655759397], + [0.4261493864669901, 2.217213369077633, 2, 0, 0.1612148713123518, 4.693189908311464, 0, -2.720233030230351, 1, 0.02599023473225814, 1.725289655759397], + [0.9324770623328013, 2.040339301342621, 2, 4.166666666666667, 0.3136678988068874, 2.144824876438837, 2.041512268408531, -0.106861264554767, 0.7186004203288798, 0.6088674213175868, 1.725289655759397], + [1, 2, 4, 0, 0.3333333333333333, 3.999999999999999, 0, -2.31845127375981, 1, 0.01234567901234551, 1.725289655759397], + [0.7091213139350294, 2.274638964597825, 1.833333333333333, 7.75, 0.238208072130221, 2.345533252336273, 3.410881111431381, 0.558113953217533, 0.5094497004116185, 0.7608688179374264, 1.725289655759397], + [0.4161749436720389, 2.583825056327961, 0, 0, 0.1387249812240129, 0, 0, 0, 1, 1, 1.725289655759397], + [0.6659596192381536, 2.256767693355746, 2.5, 6, 0.2284450217013008, 3.443359136114996, 2.639155331188279, -0.367350344747201, 0.7673619164483392, 0.5300792745888832, 1.725289655759397], + [1, 2, 0, 1, 0.3333333333333333, 0, 0.4999999999999999, 0.2898064092199763, 0.6666666666666667, 1, 1.725289655759397], + [0.459387925258634, 2.540612074741366, 1, 2, 0.1531293084195447, 2.176809500243183, 0.7872118769661439, -0.8054285949250646, 0.9368355759475115, 0.3926328355868177, 1.725289655759397], + [0.68260572574677, 2.182710391950513, 0, 5.416666666666666, 0.238230511995077, 0, 2.477393204043783, 1.327736424808056, 0.2565180128752361, 1, 1.725289655759397], + [0.6209312921230391, 2.230235398735714, 1, 2, 0.2177814766543932, 1.610484143230854, 0.8967663239197839, -0.4136799968217064, 0.8783719010971742, 0.5213872231511146, 1.725289655759397], + [0.7803173801516352, 2.212772241130693, 1, 5, 0.2603123363353145, 1.31349237295003, 2.302026965721967, 0.5631982273065281, 0.5099524183271413, 0.8358889331635316, 1.725289655759397], + [0.5250516553536253, 2.45302813924145, 1, 6, 0.1763054355717879, 1.930849168777699, 2.513667229467984, 0.5454049260406475, 0.5662130073449929, 0.777561508830334, 1.725289655759397], + [0.203181127576837, 2.790309709539656, 1, 6, 0.06787431084056803, 4.92171695238688, 2.150298936167153, -1.606349407456378, 0.9230321845151072, 0.3886057635842186, 1.725289655759397], + [0.7145233834068655, 2.170085079520931, 1, 3, 0.2477020339466259, 1.399534323470248, 1.382434277951112, -0.00991140557879785, 0.7421530662286839, 0.6796980736658556, 1.725289655759397], + [0.8025307113169092, 2.197469288683092, 1, 6, 0.2675102371056363, 1.246058232910557, 2.730413585709635, 0.860351389602304, 0.4023716041625731, 0.8868613698058293, 1.725289655759397], + [0.886960160336796, 2.113039839663204, 1, 4, 0.295653386778932, 1.127446355223306, 1.867415205641442, 0.4068397961730323, 0.5572071130808076, 0.8144379212000086, 1.725289655759397], + [0.5840734718676881, 2.415926528132312, 2.5, 5.5, 0.1946911572892293, 4.175355120340121, 2.27655929762562, -0.9098022780654729, 0.8340495404636969, 0.3957525961476541, 1.725289655759397], + [0.5268550139960962, 2.205618688973626, 0, 0, 0.1928124737023075, 0, 0, 0, 1, 1, 1.725289655759397], + [1, 1.954150177116668, 1, 3, 0.3385068260057204, 0.9999999999999998, 1.535194190871489, 0.3102054133837139, 0.5833958240116991, 0.8085296778030449, 1.725289655759397], + [0.7013114701420603, 2.186058834646364, 0, 2, 0.2428893408576666, 0, 0.9148884596802435, 0.530281078673453, 0.5732165501869386, 1, 1.725289655759397], + [0.6103766338418385, 2.230395005807139, 1, 2, 0.2148629707938298, 1.638332702393587, 0.8967021513197104, -0.4298585739491048, 0.8813404805118064, 0.5160100083098675, 1.725289655759397], + [1, 2, 0, 0, 0.3333333333333333, 0, 0, 0, 1, 1, 1.725289655759397], + [1.416174943672039, 1.583825056327961, 0, 0, 0.4720583145573463, 0, 0, 0, 1, 1, 1.725289655759397], + [0.566048512190645, 2.41804757094315, 2, 3, 0.1896884337572, 3.533266066295039, 1.240670380537576, -1.333516642795554, 0.9504034442939914, 0.2397204872545077, 1.725289655759397] + ] + } + }, + "tested":{ + "0":{ + "Baboon":"test", + "Cat":"test", + "Chimp":"test", + "Cow":"test", + "Horse":"test", + "Human":"test", + "Mouse":"test", + "Node1":"test", + "Node12":"test", + "Node2":"test", + "Node3":"test", + "Node8":"test", + "Node9":"test", + "Pig":"test", + "Rat":"test", + "RhMonkey":"test" + } + }, + "timers":{ + "Ancestor sampling analysis":{ + "order":3, + "timer":12 + }, + "Model fitting":{ + "order":1, + "timer":1 + }, + "Primary SLAC analysis":{ + "order":2, + "timer":1 + }, + "Total time":{ + "order":0, + "timer":14 + } + } +} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-in1.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in1.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,152 @@ +#NEXUS +begin taxa; + dimensions ntax=50; + taxlabels + C019-B2_10_1[&!color=#ff0000] + C019-B2_13_1[&!color=#ff0000] + C019-B2_16_1[&!color=#ff0000] + C019-B2_17_3[&!color=#ff0000] + C019-B2_18_1[&!color=#ff0000] + C019-B2_1_2[&!color=#ff0000] + C019-B2_24_1[&!color=#ff0000] + C019-B2_28_1[&!color=#ff0000] + C019-B2_29_1[&!color=#ff0000] + C019-B2_31_1[&!color=#ff0000] + C019-B2_32_1[&!color=#ff0000] + C019-B2_34_1[&!color=#ff0000] + C019-B2_35_1[&!color=#ff0000] + C019-B2_42_2[&!color=#ff0000] + C019-B2_43_2[&!color=#ff0000] + C019-B2_45_1[&!color=#ff0000] + C019-B2_46_2[&!color=#ff0000] + C019-B2_47_3[&!color=#ff0000] + C019-B2_4_1[&!color=#ff0000] + C019-B2_52_1[&!color=#ff0000] + C019-B2_53_1[&!color=#ff0000] + C019-B2_54_1[&!color=#ff0000] + C019-B2_5_1[&!color=#ff0000] + C019-B2_6_3[&!color=#ff0000] + C019-B2_9_1[&!color=#ff0000] + C019-S2_10_1[&!color=#0000ff] + C019-S2_11_1[&!color=#0000ff] + C019-S2_12_2[&!color=#0000ff] + C019-S2_13_1[&!color=#0000ff] + C019-S2_14_1[&!color=#0000ff] + C019-S2_15_4[&!color=#0000ff] + C019-S2_16_1[&!color=#0000ff] + C019-S2_17_1[&!color=#0000ff] + C019-S2_18_2[&!color=#0000ff] + C019-S2_19_1[&!color=#0000ff] + C019-S2_1_1[&!color=#0000ff] + C019-S2_20_2[&!color=#0000ff] + C019-S2_21_1[&!color=#0000ff] + C019-S2_22_1[&!color=#0000ff] + C019-S2_23_2[&!color=#0000ff] + C019-S2_24_1[&!color=#0000ff] + C019-S2_25_2[&!color=#0000ff] + C019-S2_2_1[&!color=#0000ff] + C019-S2_3_1[&!color=#0000ff] + C019-S2_4_1[&!color=#0000ff] + C019-S2_5_1[&!color=#0000ff] + C019-S2_6_1[&!color=#0000ff] + C019-S2_7_1[&!color=#0000ff] + C019-S2_8_1[&!color=#0000ff] + C019-S2_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] ((((((C019-B2_35_1:0.005858,C019-B2_52_1:0.001773):9.4E-4,((((((C019-B2_28_1:0.002896,C019-B2_29_1:9.09E-4):0.004372,C019-B2_31_1:0.003387):0.001252,C019-S2_9_1:0.001965):4.28E-4,C019-B2_34_1:0.003365):0.00173,C019-S2_2_1:0.011763):5.94E-4,((((C019-B2_4_1:0.002924,C019-B2_6_3:8.81E-4):0.001821,C019-B2_5_1:0.001994):0.006052,C019-S2_1_1:0.011533):0.002707,((C019-S2_4_1:0.006447,C019-S2_6_1:0.00696):0.001115,C019-S2_7_1:0.004624):0.003256):0.001452):0.002006):3.96E-4,((C019-S2_10_1:0.005429,C019-S2_12_2:3.52E-4):9.31E-4,C019-B2_42_2:9.87E-4):6.51E-4):5.28E-4,(C019-B2_53_1:0.002654,C019-B2_54_1:0.001151):0.002202):3.98E-4,((((((C019-B2_9_1:0.003599,C019-B2_10_1:0.002149):0.003701,C019-B2_1_2:0.011845):0.001658,C019-S2_3_1:0.009874):1.58E-4,C019-S2_5_1:0.009998):2.67E-4,(((C019-B2_17_3:0.0,C019-S2_22_1:0.0):6.76E-4,C019-B2_16_1:0.003129):2.62E-4,(((((C019-B2_18_1:0.0,C019-S2_25_2:0.0):3.0E-5,C019-S2_24_1:-3.0E-5):7.69E-4,C019-S2_23_2:0.003047):4.93E-4,(((((C019-B2_24_1:0.004304,C019-S2_19_1:-0.002103):0.00459,C019-S2_17_1:0.00129):0.002822,C019-S2_18_2:0.004477):8.52E-4,C019-S2_21_1:0.001446):8.3E-4,C019-S2_20_2:0.003028):0.002252):0.001275,C019-B2_13_1:0.006181):9.2E-4):0.003349):0.001411,C019-S2_13_1:-4.68E-4):0.001963):3.46E-4,(((C019-B2_45_1:8.37E-4,C019-S2_8_1:0.006794):0.001393,C019-S2_14_1:5.17E-4):3.77E-4,(((C019-B2_32_1:0.005635,C019-B2_43_2:0.001995):9.13E-4,C019-S2_11_1:0.002993):5.52E-4,(((C019-B2_46_2:0.0,C019-S2_15_4:0.0):0.001576,C019-S2_16_1:0.002229):0.001073,C019-B2_47_3:8.77E-4):8.62E-4):7.32E-4):3.46E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-in2.nhx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-in2.nhx Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,166 @@ +#NEXUS +begin taxa; + dimensions ntax=64; + taxlabels + C019-B3_103_1[&!color=#ff0000] + C019-B3_10_1[&!color=#ff0000] + C019-B3_121_1[&!color=#ff0000] + C019-B3_122_4[&!color=#ff0000] + C019-B3_125_1[&!color=#ff0000] + C019-B3_132_1[&!color=#ff0000] + C019-B3_140_2[&!color=#ff0000] + C019-B3_144_1[&!color=#ff0000] + C019-B3_147_1[&!color=#ff0000] + C019-B3_154_1[&!color=#ff0000] + C019-B3_162_1[&!color=#ff0000] + C019-B3_164_1[&!color=#ff0000] + C019-B3_173_1[&!color=#ff0000] + C019-B3_179_1[&!color=#ff0000] + C019-B3_180_1[&!color=#ff0000] + C019-B3_18_1[&!color=#ff0000] + C019-B3_1_1[&!color=#ff0000] + C019-B3_201_1[&!color=#ff0000] + C019-B3_211_4[&!color=#ff0000] + C019-B3_26_6[&!color=#ff0000] + C019-B3_27_1[&!color=#ff0000] + C019-B3_32_1[&!color=#ff0000] + C019-B3_37_1[&!color=#ff0000] + C019-B3_3_2[&!color=#ff0000] + C019-B3_57_1[&!color=#ff0000] + C019-B3_59_1[&!color=#ff0000] + C019-B3_61_3[&!color=#ff0000] + C019-B3_63_1[&!color=#ff0000] + C019-B3_84_1[&!color=#ff0000] + C019-B3_87_1[&!color=#ff0000] + C019-B3_94_1[&!color=#ff0000] + C019-B3_98_1[&!color=#ff0000] + C019-S3_10_3[&!color=#0000ff] + C019-S3_11_1[&!color=#0000ff] + C019-S3_12_1[&!color=#0000ff] + C019-S3_13_1[&!color=#0000ff] + C019-S3_14_1[&!color=#0000ff] + C019-S3_15_1[&!color=#0000ff] + C019-S3_16_1[&!color=#0000ff] + C019-S3_17_1[&!color=#0000ff] + C019-S3_18_1[&!color=#0000ff] + C019-S3_19_2[&!color=#0000ff] + C019-S3_1_3[&!color=#0000ff] + C019-S3_20_1[&!color=#0000ff] + C019-S3_21_1[&!color=#0000ff] + C019-S3_22_2[&!color=#0000ff] + C019-S3_23_6[&!color=#0000ff] + C019-S3_24_1[&!color=#0000ff] + C019-S3_25_1[&!color=#0000ff] + C019-S3_26_1[&!color=#0000ff] + C019-S3_27_1[&!color=#0000ff] + C019-S3_28_1[&!color=#0000ff] + C019-S3_29_1[&!color=#0000ff] + C019-S3_2_1[&!color=#0000ff] + C019-S3_30_5[&!color=#0000ff] + C019-S3_31_1[&!color=#0000ff] + C019-S3_32_1[&!color=#0000ff] + C019-S3_3_1[&!color=#0000ff] + C019-S3_4_1[&!color=#0000ff] + C019-S3_5_1[&!color=#0000ff] + C019-S3_6_1[&!color=#0000ff] + C019-S3_7_44[&!color=#0000ff] + C019-S3_8_1[&!color=#0000ff] + C019-S3_9_1[&!color=#0000ff] +; +end; + +begin trees; + tree tree_1 = [&R] (((((((C019-S3_30_5:0.001628,C019-S3_29_1:0.006003):0.00113,(C019-B3_173_1:0.001171,C019-S3_28_1:0.002634):0.001744):8.3E-4,C019-B3_132_1:0.014016):5.86E-4,((C019-S3_25_1:0.002323,C019-S3_26_1:0.001482):9.35E-4,C019-B3_144_1:0.004793):0.001476):5.2E-4,((C019-B3_140_2:0.005006,C019-B3_211_4:7.09E-4):0.005792,C019-S3_24_1:0.003793):6.51E-4):3.29E-4,((((((C019-B3_180_1:0.007012,C019-S3_12_1:0.002539):0.001059,C019-B3_164_1:0.004685):0.001059,C019-B3_201_1:0.002755):4.7E-4,C019-S3_27_1:0.004308):5.29E-4,(C019-B3_179_1:0.00111,C019-B3_162_1:0.006521):0.001397):4.5E-4,(((C019-B3_98_1:0.00603,C019-B3_84_1:0.011255):0.001462,C019-B3_3_2:0.01022):0.004778,(((((C019-B3_122_4:-1.5E-5,C019-B3_121_1:0.003821):1.07E-4,(((C019-S3_6_1:3.19E-4,C019-S3_5_1:0.003493):2.06E-4,C019-S3_4_1:0.003609):1.56E-4,C019-S3_7_44:-1.63E-4):0.001868):8.3E-5,C019-S3_2_1:0.003743):9.49E-4,C019-S3_3_1:9.47E-4):1.32E-4,((((((C019-B3_87_1:0.004026,C019-B3_94_1:0.003649):0.001868,C019-S3_9_1:0.001947):5.6E-5,C019-S3_8_1:0.001847):0.002662,C019-S3_10_3:0.003074):0.001087,C019-B3_103_1:0.002733):2.29E-4,(C019-S3_1_3:0.003978,C019-B3_125_1:0.003697):9.13E-4):4.97E-4):0.006645):7.82E-4):8.25E-4):5.47E-4,((((C019-S3_22_2:9.84E-4,C019-S3_23_6:0.005041):0.001644,(((((((((C019-B3_32_1:0.001955,C019-S3_15_1:-5.5E-5):9.11E-4,C019-B3_37_1:9.97E-4):0.001209,C019-B3_57_1:0.002666):0.001047,C019-B3_59_1:0.001825):0.001321,(C019-B3_26_6:-2.4E-5,C019-B3_27_1:2.4E-5):0.006853):0.001793,C019-B3_10_1:0.009272):0.001166,((C019-S3_19_2:7.58E-4,C019-S3_17_1:0.003048):0.001952,C019-S3_11_1:0.007625):0.001734):0.001109,C019-B3_147_1:0.00437):0.001515,(((C019-S3_32_1:0.009024,C019-S3_31_1:0.002453):0.007605,C019-B3_1_1:0.014729):0.003341,(C019-S3_14_1:0.002908,C019-S3_13_1:0.004722):0.006888):0.001642):0.00149):2.85E-4,(((C019-S3_20_1:4.17E-4,C019-S3_21_1:0.001505):0.001098,C019-S3_16_1:0.00369):0.00156,((C019-B3_61_3:7.33E-4,C019-B3_63_1:0.006898):0.003303,C019-B3_18_1:0.0063):0.00288):7.85E-4):1.97E-4,(C019-S3_18_1:3.32E-4,C019-B3_154_1:0.00368):0.001664):5.47E-4); +end; + +begin figtree; + set appearance.backgroundColorAttribute="Default"; + set appearance.backgroundColour=#ffffff; + set appearance.branchColorAttribute="User selection"; + set appearance.branchColorGradient=false; + set appearance.branchLineWidth=1.0; + set appearance.branchMinLineWidth=0.0; + set appearance.branchWidthAttribute="Fixed"; + set appearance.foregroundColour=#000000; + set appearance.hilightingGradient=false; + set appearance.selectionColour=#2d3680; + set branchLabels.colorAttribute="User selection"; + set branchLabels.displayAttribute="Branch times"; + set branchLabels.fontName="sansserif"; + set branchLabels.fontSize=8; + set branchLabels.fontStyle=0; + set branchLabels.isShown=false; + set branchLabels.significantDigits=4; + set layout.expansion=0; + set layout.layoutType="RECTILINEAR"; + set layout.zoom=0; + set legend.attribute=null; + set legend.fontSize=10.0; + set legend.isShown=false; + set legend.significantDigits=4; + set nodeBars.barWidth=4.0; + set nodeBars.displayAttribute=null; + set nodeBars.isShown=false; + set nodeLabels.colorAttribute="User selection"; + set nodeLabels.displayAttribute="Node ages"; + set nodeLabels.fontName="sansserif"; + set nodeLabels.fontSize=8; + set nodeLabels.fontStyle=0; + set nodeLabels.isShown=false; + set nodeLabels.significantDigits=4; + set nodeShapeExternal.colourAttribute="User selection"; + set nodeShapeExternal.isShown=false; + set nodeShapeExternal.minSize=10.0; + set nodeShapeExternal.scaleType=Width; + set nodeShapeExternal.shapeType=Circle; + set nodeShapeExternal.size=4.0; + set nodeShapeExternal.sizeAttribute="Fixed"; + set nodeShapeInternal.colourAttribute="User selection"; + set nodeShapeInternal.isShown=false; + set nodeShapeInternal.minSize=10.0; + set nodeShapeInternal.scaleType=Width; + set nodeShapeInternal.shapeType=Circle; + set nodeShapeInternal.size=4.0; + set nodeShapeInternal.sizeAttribute="Fixed"; + set polarLayout.alignTipLabels=false; + set polarLayout.angularRange=0; + set polarLayout.rootAngle=0; + set polarLayout.rootLength=100; + set polarLayout.showRoot=true; + set radialLayout.spread=0.0; + set rectilinearLayout.alignTipLabels=false; + set rectilinearLayout.curvature=0; + set rectilinearLayout.rootLength=100; + set scale.offsetAge=0.0; + set scale.rootAge=1.0; + set scale.scaleFactor=1.0; + set scale.scaleRoot=false; + set scaleAxis.automaticScale=true; + set scaleAxis.fontSize=8.0; + set scaleAxis.isShown=false; + set scaleAxis.lineWidth=1.0; + set scaleAxis.majorTicks=1.0; + set scaleAxis.minorTicks=0.5; + set scaleAxis.origin=0.0; + set scaleAxis.reverseAxis=false; + set scaleAxis.showGrid=true; + set scaleBar.automaticScale=true; + set scaleBar.fontSize=10.0; + set scaleBar.isShown=true; + set scaleBar.lineWidth=1.0; + set scaleBar.scaleRange=0.0; + set tipLabels.colorAttribute="User selection"; + set tipLabels.displayAttribute="Names"; + set tipLabels.fontName="sansserif"; + set tipLabels.fontSize=8; + set tipLabels.fontStyle=0; + set tipLabels.isShown=true; + set tipLabels.significantDigits=4; + set trees.order=false; + set trees.orderType="increasing"; + set trees.rooting=false; + set trees.rootingType="User Selection"; + set trees.transform=false; + set trees.transformType="cladogram"; +end; + diff -r 000000000000 -r 7c86ceaf523c test-data/sm19-out1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sm19-out1.json Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,2606 @@ +{ + "compartments":2, + "events":{ + "C019-B2_18_1":{ + "from":"Semen", + "to":"Blood" + }, + "C019-B2_24_1":{ + "from":"Semen", + "to":"Blood" + }, + "C019-B2_45_1":{ + "from":"Semen", + "to":"Blood" + }, + "C019-B2_46_2":{ + "from":"Semen", + "to":"Blood" + }, + "C019-B2_47_3":{ + "from":"Semen", + "to":"Blood" + }, + "C019-S2_1_1":{ + "from":"Blood", + "to":"Semen" + }, + "C019-S2_22_1":{ + "from":"Blood", + "to":"Semen" + }, + "C019-S2_2_1":{ + "from":"Blood", + "to":"Semen" + }, + "C019-S2_9_1":{ + "from":"Blood", + "to":"Semen" + }, + "Node2":{ + "from":"Semen", + "to":"Blood" + }, + "Node28":{ + "from":"Blood", + "to":"Semen" + }, + "Node34":{ + "from":"Blood", + "to":"Semen" + }, + "Node45":{ + "from":"Semen", + "to":"Blood" + }, + "Node52":{ + "from":"Semen", + "to":"Blood" + }, + "Node59":{ + "from":"Blood", + "to":"Semen" + }, + "Node88":{ + "from":"Semen", + "to":"Blood" + } + }, + "leaf-count":50, + "migrations":16, + "node-migrations":{ + "Node10":1, + "Node11":1, + "Node12":0, + "Node13":0, + "Node2":6, + "Node20":2, + "Node21":1, + "Node22":0, + "Node23":0, + "Node28":1, + "Node29":0, + "Node3":5, + "Node33":1, + "Node34":1, + "Node38":0, + "Node4":4, + "Node41":6, + "Node42":6, + "Node43":1, + "Node44":1, + "Node45":1, + "Node46":0, + "Node5":0, + "Node52":5, + "Node53":1, + "Node54":1, + "Node58":3, + "Node59":3, + "Node60":1, + "Node61":1, + "Node62":1, + "Node67":1, + "Node68":1, + "Node69":1, + "Node70":1, + "Node71":1, + "Node79":16, + "Node8":4, + "Node80":4, + "Node81":1, + "Node82":1, + "Node86":3, + "Node87":1, + "Node88":1, + "Node9":2, + "Node92":2, + "Node93":1, + "Node94":1 + }, + "node-p-value":{ + "panmictic":{ + "Node10":0.3866133866133866, + "Node11":0.6103896103896104, + "Node12":0.1568431568431568, + "Node13":0.3486513486513487, + "Node2":0.4045954045954046, + "Node20":0.5954045954045954, + "Node21":0.6183816183816184, + "Node22":0.1538461538461539, + "Node23":0.3626373626373626, + "Node28":0.9050949050949051, + "Node29":0.3786213786213786, + "Node3":0.2897102897102897, + "Node33":0.8901098901098901, + "Node34":1, + "Node38":0.3966033966033966, + "Node4":0.2787212787212787, + "Node41":0.3816183816183816, + "Node42":0.4715284715284715, + "Node43":0.3926073926073926, + "Node44":0.6113886113886113, + "Node45":0.8561438561438561, + "Node46":0.4015984015984016, + "Node5":0.3886113886113886, + "Node52":0.7592407592407593, + "Node53":0.8971028971028971, + "Node54":1, + "Node58":0.3706293706293706, + "Node59":0.5024975024975025, + "Node60":0.5954045954045954, + "Node61":0.8671328671328671, + "Node62":1, + "Node67":0.2117882117882118, + "Node68":0.3646353646353646, + "Node69":0.5784215784215784, + "Node70":0.8501498501498501, + "Node71":1, + "Node79":0.3846153846153846, + "Node8":0.5424575424575424, + "Node80":0.926073926073926, + "Node81":0.8901098901098901, + "Node82":1, + "Node86":0.967032967032967, + "Node87":0.8901098901098901, + "Node88":1, + "Node9":0.7902097902097902, + "Node92":1, + "Node93":0.8721278721278721, + "Node94":1 + }, + "structured":{ + "Node10":0.935064935064935, + "Node11":1, + "Node12":0.8671328671328671, + "Node13":1, + "Node2":0.7232767232767233, + "Node20":0.9760239760239761, + "Node21":1, + "Node22":0.8731268731268731, + "Node23":1, + "Node28":0.9050949050949051, + "Node29":1, + "Node3":0.9100899100899101, + "Node33":1, + "Node34":1, + "Node38":1, + "Node4":0.936063936063936, + "Node41":0.7002997002997003, + "Node42":0.8021978021978022, + "Node43":0.9410589410589411, + "Node44":1, + "Node45":0.8561438561438561, + "Node46":1, + "Node5":1, + "Node52":0.7592407592407593, + "Node53":1, + "Node54":1, + "Node58":0.8061938061938062, + "Node59":0.9170829170829171, + "Node60":1, + "Node61":0.8671328671328671, + "Node62":1, + "Node67":0.7602397602397603, + "Node68":0.929070929070929, + "Node69":1, + "Node70":0.8501498501498501, + "Node71":1, + "Node79":0.7822177822177823, + "Node8":0.8871128871128872, + "Node80":1, + "Node81":1, + "Node82":1, + "Node86":0.967032967032967, + "Node87":0.8901098901098901, + "Node88":1, + "Node9":0.7902097902097902, + "Node92":1, + "Node93":1, + "Node94":1 + } + }, + "p-value":{ + "panmictic":0.3846153846153846, + "structured":0.7822177822177823 + }, + "partition-counts":{ + "Blood":25, + "Semen":25 + }, + "partitions":{ + "Blood":{ + "0":"C019-B2_35_1", + "1":"C019-B2_52_1", + "10":"C019-B2_53_1", + "11":"C019-B2_54_1", + "12":"C019-B2_9_1", + "13":"C019-B2_10_1", + "14":"C019-B2_1_2", + "15":"C019-B2_17_3", + "16":"C019-B2_16_1", + "17":"C019-B2_18_1", + 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+} \ No newline at end of file diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-in1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,260 @@ +>NC_045512.2:21563-25384 +ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT 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+------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------CGAGACG +>epi_isl_1041400/hCoV-19/USA/NY-PRL-2021_02_08_05H02/2021 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------A +>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021 +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +--------------------------------------A diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-in2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-in2.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,455 @@ +>NC_045512.2:21563-25384 +ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4 +CTTGTTTTTTTTTTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGATTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCTATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1 +ATGTATGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGTAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW206333_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2009646_2020_Segment_null_4 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGATATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTTAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACCACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATTGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACC +AGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGAC +AAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCC +AATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGAT +AACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATA +ATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTT +AATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTT +TTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTAT +TCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAA +GGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTAT +TTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTT +TCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACT +TTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCT +GGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAAT +GAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAG +TGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTC +CAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAA +GTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAAC +TGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTAT +GGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTT +GTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGAT +TATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAAT +CTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAAT +CTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGT +AATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACT +AATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCA +CCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAAT +TTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTG +CCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG +ACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCA +GGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTC +CCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCT +AATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATAT +GAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCT +CCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGT +GCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATT +AGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATG +TACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGT +ACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAA +GTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTT +AATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGAT +CTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGC +CTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTT +TTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGT +ACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATG +CAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAA +AAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCC +ACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAAC +ACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATC +CTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGA +CTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCT +TCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTT +GATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTA +GTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCC +ATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACA +CACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACA +TTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCT +TTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACA +TCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAA +AAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTC +CAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTT +ATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGC +TGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGAC +TCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-out1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out1.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,8 @@ +>NC_045512.2:21563-25384 +ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>epi_isl_1041406/hCoV-19/USA/NY-PRL-2021_02_08_05H12/2021 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGACG +>epi_isl_1041400/hCoV-19/USA/NY-PRL-2021_02_08_05H02/2021 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>epi_isl_1041403/hCoV-19/USA/NY-PRL-2021_02_08_05H08/2021 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- diff -r 000000000000 -r 7c86ceaf523c test-data/strike-ambigs-out2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strike-ambigs-out2.fa Tue Apr 20 10:27:46 2021 +0000 @@ -0,0 +1,14 @@ +>NC_045512.2:21563-25384 +ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGATGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW540268_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MA_MASPHL_01380_2020_Segment_null_4 +CTTGTTTTTTTTTTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGATTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCTATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW467454_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_EGY_EGY_CCHE57357_A_46_2020_Segment_null_1 +ATGTATGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGTAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MT496989_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_IND_GBRC63_2020_Segment_null_3 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW206333_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_UT_UPHL_2009646_2020_Segment_null_4 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGATATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW525081_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_MO_CDC_STM_0000025_G03_2021_Segment_null_1 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTTATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACCACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATTGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA +>gb_MW518841_Organism_Severe_acute_respiratory_syndrome_coronavirus_2_Strain_Name_SARS_CoV_2_human_USA_CA_CDC_STM_220_2020_Segment_null_1 +ATGTTAGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTTGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATCATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCACTGTAGAAAAAGGAATCTATCAAACTTCTAACTTTAGAGTCCAACCAACAGAATCTATTGTTAGATTTCCTAATATTACAAACTTGTGCCCTTTTGGTGAAGTTTTTAACGCCACCAGATTTGCATCTGTTTATGCTTGGAACAGGAAGAGAATCAGCAACTGTGTTGCTGATTATTCTGTCCTATATAATTCCGCATCATTTTCCACTTTTAAGTGTTATGGAGTGTCTCCTACTAAATTAAATGATCTCTGCTTTACTAATGTCTATGCAGATTCATTTGTAATTAGAGGTGATGAAGTCAGACAAATCGCTCCAGGGCAAACTGGAAAGATTGCTGATTATAATTATAAATTACCAGATGATTTTACAGGCTGCGTTATAGCTTGGAATTCTAACAATCTTGATTCTAAGGTTGGTGGTAATTATAATTACCTGTATAGATTGTTTAGGAAGTCTAATCTCAAACCTTTTGAGAGAGATATTTCAACTGAAATCTATCAGGCCGGTAGCACACCTTGTAATGGTGTTGAAGGTTTTAATTGTTACTTTCCTTTACAATCATATGGTTTCCAACCCACTAATGGTGTTGGTTACCAACCATACAGAGTAGTAGTACTTTCTTTTGAACTTCTACATGCACCAGCAACTGTTTGTGGACCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTTAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAGACACTTGAGATTCTTGACATTACACCATGTTCTTTTGGTGGTGTCAGTGTTATAACACCAGGAACAAATACTTCTAACCAGGTTGCTGTTCTTTATCAGGGTGTTAACTGCACAGAAGTCCCTGTTGCTATTCATGCAGATCAACTTACTCCTACTTGGCGTGTTTATTCTACAGGTTCTAATGTTTTTCAAACACGTGCAGGCTGTTTAATAGGGGCTGAACATGTCAACAACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCATACCCACAAATTTTACTATTAGTGTTACCACAGAAATTCTACCAGTGTCTATGACCAAGACATCAGTAGATTGTACAATGTACATTTGTGGTGATTCAACTGAATGCAGCAATCTTTTGTTGCAATATGGCAGTTTTTGTACACAATTAAACCGTGCTTTAACTGGAATAGCTGTTGAACAAGACAAAAACACCCAAGAAGTTTTTGCACAAGTCAAACAAATTTACAAAACACCACCAATTAAAGATTTTGGTGGTTTTAATTTTTCACAAATATTACCAGATCCATCAAAACCAAGCAAGAGGTCATTTATTGAAGATCTACTTTTCAACAAAGTGACACTTGCAGATGCTGGCTTCATCAAACAATATGGTGATTGCCTTGGTGATATTGCTGCTAGAGACCTCATTTGTGCACAAAAGTTTAACGGCCTTACTGTTTTGCCACCTTTGCTCACAGATGAAATGATTGCTCAATACACTTCTGCACTGTTAGCGGGTACAATCACTTCTGGTTGGACCTTTGGTGCAGGTGCTGCATTACAAATACCATTTGCTATGCAAATGGCTTATAGGTTTAATGGTATTGGAGTTACACAGAATGTTCTCTATGAGAACCAAAAATTGATTGCCAACCAATTTAATAGTGCTATTGGCAAAATTCAAGACTCACTTTCTTCCACAGCAAGTGCACTTGGAAAACTTCAAGATGTGGTCAACCAAAATGCACAAGCTTTAAACACGCTTGTTAAACAACTTAGCTCCAATTTTGGTGCAATTTCAAGTGTTTTAAATGATATCCTTTCACGTCTTGACAAAGTTGAGGCTGAAGTGCAAATTGATAGGTTGATCACAGGCAGACTTCAAAGTTTGCAGACATATGTGACTCAACAATTAATTAGAGCTGCAGAAATCAGAGCTTCTGCTAATCTTGCTGCTACTAAAATGTCAGAGTGTGTACTTGGACAATCAAAAAGAGTTGATTTTTGTGGAAAGGGCTATCATCTTATGTCCTTCCCTCAGTCAGCACCTCATGGTGTAGTCTTCTTGCATGTGACTTATGTCCCTGCACAAGAAAAGAACTTCACAACTGCTCCTGCCATTTGTCATGATGGAAAAGCACACTTTCCTCGTGAAGGTGTCTTTGTTTCAAATGGCACACACTGGTTTGTAACACAAAGGAATTTTTATGAACCACAAATCATTACTACAGACAACACATTTGTGTCTGGTAACTGTGATGTTGTAATAGGAATTGTCAACAACACAGTTTATGATCCTTTGCAACCTGAATTAGACTCATTCAAGGAGGAGTTAGATAAATATTTTAAGAATCATACATCACCAGATGTTGATTTAGGTGACATCTCTGGCATTAATGCTTCAGTTGTAAACATTCAAAAAGAAATTGACCGCCTCAATGAGGTTGCCAAGAATTTAAATGAATCTCTCATCGATCTCCAAGAACTTGGAAAGTATGAGCAGTATATAAAATGGCCATGGTACATTTGGCTAGGTTTTATAGCTGGCTTGATTGCCATAGTAATGGTGACAATTATGCTTTGCTGTATGACCAGTTGCTGTAGTTGTCTCAAGGGCTGTTGTTCTTGTGGATCCTGCTGCAAATTTGATGAAGACGACTCTGAGCCAGTGCTCAAAGGAGTCAAATTACATTACACA