# HG changeset patch # User iuc # Date 1660831269 0 # Node ID 4515f2f64e135179edb6fc0bad1cd620cb3a5a1d # Parent 5b6b8b08f1a9ed106f89afd55a6c41f0880825fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 821e0f3e4546bc55e093ab63bd9f9b57f2bf772d diff -r 5b6b8b08f1a9 -r 4515f2f64e13 test-data/relax-in1.fa --- a/test-data/relax-in1.fa Wed Mar 30 00:17:25 2022 +0000 +++ b/test-data/relax-in1.fa Thu Aug 18 14:01:09 2022 +0000 @@ -1,20 +1,8 @@ ->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 5b6b8b08f1a9 -r 4515f2f64e13 test-data/relax-in1.nhx --- a/test-data/relax-in1.nhx Wed Mar 30 00:17:25 2022 +0000 +++ b/test-data/relax-in1.nhx Thu Aug 18 14:01:09 2022 +0000 @@ -1,1 +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 +(((Pig:0.147969,Cow{TEST}:0.21343):0.085099,Baboon:0.011873):0.340802,Rat:0.050958) diff -r 5b6b8b08f1a9 -r 4515f2f64e13 test-data/relax-in2.nex --- a/test-data/relax-in2.nex Wed Mar 30 00:17:25 2022 +0000 +++ b/test-data/relax-in2.nex Thu Aug 18 14:01:09 2022 +0000 @@ -8,7 +8,7 @@ BEGIN TAXA; DIMENSIONS NTAX = 10; TAXLABELS - 'Human' 'Chimp' 'Baboon' 'RhMonkey' 'Cow' 'Pig' 'Horse' 'Cat' 'Mouse' 'Rat' ; + 'Baboon' 'Cow' 'Pig' 'Rat' ; END; BEGIN CHARACTERS; @@ -21,20 +21,14 @@ ; MATRIX - '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; END; BEGIN TREES; - TREE tree = ((((Pig:0.147969,Cow:0.213430):0.085099,Horse:0.165787,Cat:0.264806):0.058611,((RhMonkey{PR}:0.002015,Baboon{PR}:0.003108){PR}:0.022733,(Human{PR}:0.004349,Chimp{PR}:0.000799){PR}:0.011873){PR}:0.101856){PR}:0.340802,Rat:0.050958,Mouse:0.097950); + TREE tree = (((Pig:0.147969,Cow:0.213430):0.085099,Baboon{PR}:0.003108){PR}:0.340802,Rat:0.050958); END; BEGIN HYPHY; @@ -42,7 +36,7 @@ DATA_PANEL_SOURCE_PATH=""; DataSet CD2 = ReadDataFile (USE_NEXUS_FILE_DATA); DataSetFilter CD2_part = CreateFilter (CD2,3,"0-560","(null)","TAA,TAG,TGA"); -Tree CD2_tree=((((Pig,Cow)Node3,Horse,Cat)Node2,((RhMonkey,Baboon)Node9,(Human,Chimp)Node12)Node8)Node1,Rat,Mouse); +Tree CD2_tree=(((Pig,Cow)Node2,Baboon)Node1,Rat); OpenDataPanel(CD2,"(null)","0,0,0,0,2,0,10","MG94xREV_3x4,6,0,14443523,CD2_tree",CD2_LF); global CD2_part_Shared_AC=0.5710714109234631; @@ -50,36 +44,16 @@ global CD2_part_Shared_CG=0.4456308760366715; global CD2_part_Shared_CT=0.9454291760502562; global CD2_part_Shared_GT=0.3224080259059006; -CD2_tree.Node12.synRate=0.08168540352543764; -CD2_tree.Node8.nonSynRate=0.2938890030949185; -CD2_tree.Human.synRate=1e-30; CD2_tree.Baboon.nonSynRate=0; CD2_tree.Baboon.synRate=0.01716650886630832; -CD2_tree.Node12.nonSynRate=0.02962786133931161; -CD2_tree.Chimp.synRate=1e-30; -CD2_tree.Chimp.nonSynRate=0.005834136861061837; -CD2_tree.Node9.nonSynRate=0.0433794394076959; -CD2_tree.Human.nonSynRate=0; -CD2_tree.Node9.synRate=0.1139808847086709; -CD2_tree.Node8.synRate=0.1586154947684889; CD2_tree.Rat.synRate=0.1533251749656354; -CD2_tree.Mouse.nonSynRate=0.2332402459120736; -CD2_tree.Mouse.synRate=0.4604267094040578; CD2_tree.Rat.nonSynRate=0.1585006932449144; CD2_tree.Node1.nonSynRate=0.5097883291072822; CD2_tree.Node1.synRate=1.227004762734591; -CD2_tree.RhMonkey.synRate=0; -CD2_tree.Node3.synRate=0.1877287558837553; CD2_tree.Pig.nonSynRate=0.4826366809736332; -CD2_tree.Horse.nonSynRate=0.518627673056701; CD2_tree.Cow.nonSynRate=0.681831503936737; -CD2_tree.Cat.synRate=0.4672127128189641; -CD2_tree.Node3.nonSynRate=0.2648957141533021; -CD2_tree.Horse.synRate=0.430860769501357; CD2_tree.Pig.synRate=0.3721230153643161; CD2_tree.Node2.synRate=0.2137858662796737; -CD2_tree.RhMonkey.nonSynRate=0.01161863878954486; -CD2_tree.Cat.nonSynRate=0.7203773170684773; CD2_tree.Node2.nonSynRate=0.1379570235930709; CD2_tree.Cow.synRate=0.3646221318370894; diff -r 5b6b8b08f1a9 -r 4515f2f64e13 test-data/relax-in2.nhx --- a/test-data/relax-in2.nhx Wed Mar 30 00:17:25 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -((((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 5b6b8b08f1a9 -r 4515f2f64e13 test-data/relax-out2-1.json --- a/test-data/relax-out2-1.json Wed Mar 30 00:17:25 2022 +0000 +++ b/test-data/relax-out2-1.json Thu Aug 18 14:01:09 2022 +0000 @@ -1,60 +1,55 @@ { - "Synonymous site-posteriors": [ -[0.6636913410863983, 0.4162861463391083, 0.4207669648198341, 0.5266957556553843, 0.7895328001950979, 0.9272590205679656, 0.6152945530195142, 0.7578515907144813, 0.1238947876214084, 0.3018037085532145, 0.2282864078469784, 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(general descriptive)":0.5371848217199983 }, "Node3":{ - "General descriptive":0.1330256319960288, + "General descriptive":0.1330354609631224, "MG94xREV with separate rates for branch sets":0.1003154990002797, "Nucleotide GTR":0.09883748387954429, - "RELAX alternative":0.1378173139909468, - "RELAX null":0.1387701954254672, - "RELAX partitioned descriptive":0.136719474302551, - "k (general descriptive)":1.981625732305646 + "RELAX alternative":0.1265135269643693, + "RELAX null":0.1276253046950155, + "RELAX partitioned descriptive":0.1271876163104063, + "k (general descriptive)":1.981364628056296 }, "Node8":{ - "General descriptive":0.1404338383825282, + "General descriptive":0.140369727816558, "MG94xREV with separate rates for branch sets":0.1127066220459272, "Nucleotide GTR":0.1062201244057951, - "RELAX alternative":0.1439313895033506, - "RELAX null":0.14318831284655, - "RELAX partitioned descriptive":0.1481785335086442, - "k (general descriptive)":2.211998835217187 + "RELAX alternative":0.1280322211601967, + "RELAX null":0.1343412714385626, + "RELAX partitioned descriptive":0.1406663540457613, + "k (general descriptive)":2.211767324109487 }, "Node9":{ - "General descriptive":0.02665501999328081, + "General descriptive":0.02663291940160552, "MG94xREV with separate rates for branch sets":0.02627402966233569, "Nucleotide GTR":0.02567813733543303, - "RELAX alternative":0.02985671529404269, - "RELAX null":0.02953553824738531, - "RELAX partitioned descriptive":0.02996950192160838, - "k (general descriptive)":0.07343805012797726 + "RELAX alternative":0.02720907734174326, + "RELAX null":0.02752483699250281, + "RELAX partitioned descriptive":0.02810928828288993, + "k (general descriptive)":0.07329530197274074 }, "PIG":{ - "General descriptive":0.2105401970679286, + "General descriptive":0.2104965149960229, "MG94xREV with separate rates for branch sets":0.1921302603267553, "Nucleotide GTR":0.1871390433004313, - "RELAX alternative":0.2517917117490165, - "RELAX 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descriptive":0.003670942377703963, "MG94xREV with separate rates for branch sets":0.003755247927570558, "Nucleotide GTR":0.003778804730491441, - "RELAX alternative":0.004176749981889291, - "RELAX null":0.00397871921631754, - "RELAX partitioned descriptive":0.004188079354984015, - "k (general descriptive)":5.301456309232226, + "RELAX alternative":0.003673289414323487, + "RELAX null":0.003666197747079884, + "RELAX partitioned descriptive":0.003661285250492945, + "k (general descriptive)":5.244027200799457, "original name":"RHMONKEY" } }, @@ -207,21 +202,21 @@ }, "fits":{ "General descriptive":{ - "AIC-c":6945.886057024934, - "Log Likelihood":-3420.484282637879, + "AIC-c":6945.887251511141, + "Log Likelihood":-3420.484879880983, "Rate Distributions":{ "Shared":{ "0":{ - "omega":2.201373594751134e-18, - "proportion":0.5258178735075876 + "omega":2.201644423775106e-18, + "proportion":0.1667516969215508 }, "1":{ - "omega":2.201373594751134e-18, - "proportion":0.01992025780064184 + "omega":2.201644423775106e-18, + "proportion":0.3790423141178453 }, "2":{ - "omega":2.201373412388544, - "proportion":0.4542618686917706 + "omega":2.201644241390081, + "proportion":0.4542059889606039 } } }, @@ -326,144 +321,116 @@ "estimated parameters":24 }, "RELAX alternative":{ - "AIC-c":6909.668413948684, - "Log Likelihood":-3408.69933855329, + "AIC-c":6938.419285358699, + "Log Likelihood":-3432.482965101608, "Rate Distributions":{ "Reference":{ "0":{ "omega":0, - "proportion":0.3825895192221547 + "proportion":0.2968543549269862 }, "1":{ - "omega":0.003503464580598538, - "proportion":0 + "omega":0, + "proportion":0.2447083724876047 }, "2":{ - "omega":2.417572962231385, - "proportion":0.6174104807778453 - } - }, - "Synonymous site-to-site rates":{ - "0":{ - "proportion":0.2789425737851868, - "rate":0.2834765074731829 - }, - "1":{ - "proportion":0.6311785441975573, - "rate":0.9970973177052372 - }, - "2":{ - "proportion":0.089878882017256, - "rate":3.244142488658602 + "omega":3.910413867333085, + "proportion":0.4584372725854091 } }, "Test":{ "0":{ "omega":0, - "proportion":0.3825895192221547 + "proportion":0.2968543549269862 }, "1":{ - "omega":0.9998114377116485, - "proportion":0 + "omega":0, + "proportion":0.2447083724876047 }, "2":{ - "omega":1.000029443594731, - "proportion":0.6174104807778453 + "omega":1.655264242043239, + "proportion":0.4584372725854091 } } }, "display order":2, - "estimated parameters":45 + "estimated parameters":36 }, "RELAX null":{ - "AIC-c":6919.152853316747, - "Log Likelihood":-3414.491495151524, + "AIC-c":6946.046147526199, + "Log Likelihood":-3437.336050862336, "Rate Distributions":{ "Reference":{ "0":{ - "omega":0, - "proportion":0.3885051761591228 + "omega":0.07516343499603452, + "proportion":0.2524283429126023 }, "1":{ - "omega":0.9958737025997172, - "proportion":0 + "omega":0.1730729265669467, + "proportion":0.3734402861071174 }, "2":{ - "omega":1.887643080900262, - "proportion":0.6114948238408772 - } - }, - "Synonymous site-to-site rates":{ - "0":{ - "proportion":0.2642938080646302, - "rate":0.2741590488311177 - }, - "1":{ - "proportion":0.633162055223991, - "rate":0.9728788992663913 - }, - "2":{ - "proportion":0.1025441367113787, - "rate":3.038218152856258 + "omega":3.70326279512502, + "proportion":0.3741313709802804 } }, "Test":{ "0":{ - "omega":0, - "proportion":0.3885051761591228 + "omega":0.07516343499603452, + "proportion":0.2524283429126023 }, "1":{ - "omega":0.9958737025997172, - "proportion":0 + "omega":0.1730729265669467, + "proportion":0.3734402861071174 }, "2":{ - "omega":1.887643080900262, - "proportion":0.6114948238408772 + "omega":3.70326279512502, + "proportion":0.3741313709802804 } } }, "display order":3, - "estimated parameters":44 + "estimated parameters":35 }, "RELAX partitioned descriptive":{ - "AIC-c":6917.810941882631, - "Log Likelihood":-3408.559317095162, + "AIC-c":6944.507313452719, + "Log Likelihood":-3431.356991882183, "Rate Distributions":{ "Reference":{ "0":{ - "omega":0.03550460650841439, - "proportion":0.354985198548996 + "omega":0, + "proportion":0.3694476627871225 }, "1":{ - "omega":0.05439939847728128, - "proportion":0.02231130867735708 + "omega":0.03660893085044142, + "proportion":0.1726741298596992 }, "2":{ - "omega":2.333762420535514, - "proportion":0.6227034927736469 + "omega":3.988980749944551, + "proportion":0.4578782073531784 } }, "Test":{ "0":{ - "omega":0, - "proportion":0.3705590531463396 + "omega":0.224878249826745, + "proportion":0.2953732524277409 }, "1":{ - "omega":0, - "proportion":0.06265340406614885 + "omega":0.231175241198686, + "proportion":0.5325206774143161 }, "2":{ - "omega":1.08372848194659, - "proportion":0.5667875427875115 + "omega":4.178788461910403, + "proportion":0.172106070157943 } } }, "display order":5, - "estimated parameters":49 + "estimated parameters":40 } }, "input":{ - "file name":"/tmp/tmpkgsdjj1d/job_working_directory/000/5/working/./input.nex", + "file name":"/tmp/tmps1cqwvdh/job_working_directory/000/5/working/./input.nex", "number of sequences":10, "number of sites":187, "partition count":1, @@ -471,11 +438,11 @@ "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)" } }, - "runtime":"2.5.32", + "runtime":"2.5.36", "test results":{ - "LRT":11.58431319646934, - "p-value":0.0006651049394417186, - "relaxation or intensification parameter":3.335337302186161e-05 + "LRT":9.706171521456781, + "p-value":0.001836502097725456, + "relaxation or intensification parameter":0.3695692925647034 }, "tested":{ "0":{ @@ -500,27 +467,27 @@ "timers":{ "General descriptive model fitting":{ "order":2, - "timer":105 + "timer":159 }, "Overall":{ "order":0, - "timer":3013 + "timer":428 }, "Preliminary model fitting":{ "order":1, - "timer":8 + "timer":13 }, "RELAX alternative model fitting":{ "order":3, - "timer":1229 + "timer":61 }, "RELAX null model fitting":{ "order":4, - "timer":690 + "timer":53 }, "RELAX partitioned descriptive":{ "order":5, - "timer":980 + "timer":141 } } } \ No newline at end of file