# HG changeset patch
# User iuc
# Date 1604075142 0
# Node ID 2126c9e28ce684a4c26be7cfe233eb636a438bf7
# Parent  23b9bd244670f6e8326931344e76c4228fccf9f1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"

diff -r 23b9bd244670 -r 2126c9e28ce6 hyphy_sm19.xml
--- a/hyphy_sm19.xml	Fri Sep 18 21:07:08 2020 +0000
+++ b/hyphy_sm19.xml	Fri Oct 30 16:25:42 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_sm19" name="HyPhy-SM2019" version="@VERSION@+galaxy0">
+<tool id="hyphy_sm19" name="HyPhy-SM2019" version="@VERSION@+galaxy0" profile="19.09">
     <description>Partition Tree using Modified Slatkin-Maddison Test</description>
     <macros>
         <import>macros.xml</import>
diff -r 23b9bd244670 -r 2126c9e28ce6 macros.xml
--- a/macros.xml	Fri Sep 18 21:07:08 2020 +0000
+++ b/macros.xml	Fri Oct 30 16:25:42 2020 +0000
@@ -107,14 +107,14 @@
             <yield/>
         </citations>
     </xml>
-    <token name="@VERSION@">2.5.17</token>
+    <token name="@VERSION@">2.5.21</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">hyphy</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
+    <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
     <token name="@CATCH_MPIERR@"><![CDATA[
         EC=\$? ;
         if [ \$EC -ne 0 ] ; then
diff -r 23b9bd244670 -r 2126c9e28ce6 test-data/slac-out1.json
--- a/test-data/slac-out1.json	Fri Sep 18 21:07:08 2020 +0000
+++ b/test-data/slac-out1.json	Fri Oct 30 16:25:42 2020 +0000
@@ -1,876 +1,28 @@
 {
- "analysis":{
-   "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    ",
-   "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"
-  },
- "fits":{
-   "Nucleotide GTR":{
-     "Log Likelihood":-3531.963798530155,
-     "estimated parameters":24,
-     "AIC-c":7112.142458295762,
-     "Equilibrium frequencies":[
-      [0.3563279857397504],
-      [0.1837789661319073],
-      [0.2402852049910873],
-      [0.2196078431372549]
-      ],
-     "Rate Distributions":{
-       "Substitution rate from nucleotide A to nucleotide C":0.5474490057204714,
-       "Substitution rate from nucleotide A to nucleotide G":1,
-       "Substitution rate from nucleotide A to nucleotide T":0.2645352969683238,
-       "Substitution rate from nucleotide C to nucleotide G":0.4863078374555331,
-       "Substitution rate from nucleotide C to nucleotide T":1.018028772244997,
-       "Substitution rate from nucleotide G to nucleotide T":0.3025951149895378
-      },
-     "display order":0
-    },
-   "Global MG94xREV":{
-     "Log Likelihood":-3466.724829119623,
-     "estimated parameters":31,
-     "AIC-c":6996.52909240682,
-     "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 *test*":[
-        [0.9952474740528205, 1]
-        ]
-      },
-     "display order":1
-    }
-  },
- "timers":{
-   "Total time":{
-     "timer":62,
-     "order":0
-    },
-   "Model fitting":{
-     "timer":12,
-     "order":1
-    },
-   "Primary SLAC analysis":{
-     "timer":1,
-     "order":2
-    },
-   "Ancestor sampling analysis":{
-     "timer":31,
-     "order":3
-    }
-  },
- "tested":{
-   "0":{
-     "Pig":"test",
-     "Cow":"test",
-     "Node3":"test",
-     "Horse":"test",
-     "Cat":"test",
-     "Node2":"test",
-     "RhMonkey":"test",
-     "Baboon":"test",
-     "Node9":"test",
-     "Human":"test",
-     "Chimp":"test",
-     "Node12":"test",
-     "Node8":"test",
-     "Node1":"test",
-     "Rat":"test",
-     "Mouse":"test"
-    }
-  },
- "input":{
-   "file name":"/Users/stephenshank/Documents/Data/Datamonkey/CD2.fasta",
-   "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)"
-    }
-  },
- "data partitions":{
-   "0":{
-     "name":"slac.filter.default",
-     "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]
-      ]
-    }
-  },
- "branch attributes":{
-   "0":{
-     "Human":{
-       "original name":"Human",
-       "Nucleotide GTR":0,
-       "Global MG94xREV":0,
-       "codon":[
-        ["AAA", "GAG", "ATT", "ACG", "AAT", "GCC", "TTG", "GAA", "ACC", "TGG", "GGT", "GCC", "TTG", "GGT", "CAG", "GAC", "ATC", "AAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAC", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAA", "GAG", "ACT", "TTC", "AAG", "GAA", "AAA", "GAT", "ACA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ACC", "GAT", "GAT", "CAG", "GAT", "ATC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAT", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ATA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "AAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCA", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGT", "GTC", "GAG", "CCT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"]
-        ],
-       "amino-acid":[
-        ["K", "E", "I", "T", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "N", "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", "K", "E", "K", "D", "T", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "T", "D", "D", "Q", "D", "I", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "I", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "K", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "S", "V", "E", "P", "V", "S", "C", "P", "E", "K", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ]
-      },
-     "Chimp":{
-       "original name":"Chimp",
-       "Nucleotide GTR":0.001818647577470898,
-       "Global MG94xREV":0.00182896017227404,
-       "codon":[
-        ["GAA", "GAG", "ATT", "ACG", "AAT", "GCC", "TTG", "GAA", "ACC", "TGG", "GGT", "GCC", "TTG", "GGT", "CAG", "GAC", "ATC", "AAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAC", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAA", "GAG", "ACT", "TTC", "AAG", "GAA", "AAA", "GAT", "ACA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ACC", "GAT", "GAT", "CAG", "GAT", "ATC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAT", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ATA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "AAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCA", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGT", "GTC", "GAG", "CCT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"]
-        ],
-       "amino-acid":[
-        ["E", "E", "I", "T", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "N", "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", "K", "E", "K", "D", "T", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "T", "D", "D", "Q", "D", "I", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "I", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "K", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "S", "V", "E", "P", "V", "S", "C", "P", "E", "K", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ]
-      },
-     "Baboon":{
-       "original name":"Baboon",
-       "Nucleotide GTR":0.001683434956773037,
-       "Global MG94xREV":0.001772086868294988,
-       "codon":[
-        ["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AAA", "TGG", "GAG", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"]
-        ],
-       "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", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "R", "M", "E", "T", "V", "S", "C", "P", "E", "K", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ]
-      },
-     "RhMonkey":{
-       "original name":"RhMonkey",
-       "Nucleotide GTR":0.003773669075849421,
-       "Global MG94xREV":0.00371927432647934,
-       "codon":[
-        ["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AGA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "AYT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GRC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "GTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"]
-        ],
-       "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", "R", "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", "KN", "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", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "KN", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "V", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "R", "M", "E", "T", "V", "S", "C", "P", "E", "K", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
-        ]
-      },
-     "Cow":{
-       "original name":"Cow",
-       "Nucleotide GTR":0.2483322373763571,
-       "Global MG94xREV":0.2479198638430596,
-       "codon":[
-        ["---", "---", "---", "---", "GAA", "AGC", "ATT", "GTC", "GTC", "TGG", "GGT", "GCC", "CTG", "GAT", "CAT", "GAC", "CTC", "AAC", "CTG", "GAC", "ATT", "CCT", "GGT", "TTT", "CCA", "AGA", "AGT", "GAT", "ATA", "GTG", "GCA", "GAT", "ATA", "AAA", "TGG", "AAC", "AGA", "---", "---", "AAC", "AAA", "AAC", "AAG", "ATT", "GCA", "CGA", "ATA", "AAG", "AAA", "GAT", "ATG", "CCA", "CTT", "CAC", "AAT", "GAA", "ATG", "GAC", "AAA", "TAT", "GAT", "ATG", "TTT", "ACA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "ACT", "---", "CTG", "ATG", "AGA", "AAC", "GAT", "AGT", "GGT", "CTC", "TAT", "GAG", "GTA", "GAG", "GTT", "TAT", "GAT", "TCA", "AAT", "GGA", "GTA", "AAC", "CTA", "CTG", "AGC", "AAA", "AAA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "ATG", "CTC", "TCA", "GGA", "CCT", "GAA", "ATT", "AAC", "TGG", "ATC", "TGT", "ACC", "AAC", "AGA", "ACT", "GTG", "AGC", "TGC", "AAG", "GTA", "GAA", "AAT", "GGA", "AGT", "AAT", "CCT", "AAA", "TTA", "CAA", "CTG", "TTT", "TTA", "AAT", "ACG", "ACC", "CGT", "GTC", "AAA", "CAA", "GAT", "CAT", "GGG", "AAG", "CTC", "ATC", "ACC", "TAC", "ACG", "TGG", "AAC", "ACC", "AGA", "TGG", "AAT", "AAA", "ACA", "TTC", "AAG", "TGC", "GTG", "GCG", "AGT", "AAC", "CAT", "GTC", "GAT", "AGC", "AAA", "GTC", "AGC", "ATA", "GAG", "ATC", "GCC", "GTG", "TGT", "CCA", "GAT", "GAA", "GGT", "CTG", "GAT"]
-        ],
-       "amino-acid":[
-        ["-", "-", "-", "-", "E", "S", "I", "V", "V", "W", "G", "A", "L", "D", "H", "D", "L", "N", "L", "D", "I", "P", "G", "F", "P", "R", "S", "D", "I", "V", "A", "D", "I", "K", "W", "N", "R", "-", "-", "N", "K", "N", "K", "I", "A", "R", "I", "K", "K", "D", "M", "P", "L", "H", "N", "E", "M", "D", "K", "Y", "D", "M", "F", "T", "N", "G", "T", "L", "K", "I", "K", "T", "-", "L", "M", "R", "N", "D", "S", "G", "L", "Y", "E", "V", "E", "V", "Y", "D", "S", "N", "G", "V", "N", "L", "L", "S", "K", "K", "F", "D", "L", "K", "I", "Q", "E", "M", "L", "S", "G", "P", "E", "I", "N", "W", "I", "C", "T", "N", "R", "T", "V", "S", "C", "K", "V", "E", "N", "G", "S", "N", "P", "K", "L", "Q", "L", "F", "L", "N", "T", "T", "R", "V", "K", "Q", "D", "H", "G", "K", "L", "I", "T", "Y", "T", "W", "N", "T", "R", "W", "N", "K", "T", "F", "K", "C", "V", "A", "S", "N", "H", "V", "D", "S", "K", "V", "S", "I", "E", "I", "A", "V", "C", "P", "D", "E", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.5, 0, 0, 1, 0, 0, 0.5, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.1666666666666667, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 2, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1.5, 0, 1.5, 0, 0, 1, 0, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1.5, 0, 0, 0, 1, 2, 1, 0, 0, 0, 1.5, 0, 1, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0, 1, 0, 1.5, 0, 1, 0, 1, 0, 1.5, 0, 0, 0, 1, 1, 0, 2, 0, 1, 0, 2.833333333333333, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 2, 0, 0, 0, 2, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 2, 1, 1, 0, 1, 0, 0, 2, 2.5, 0, 0, 1, 1, 0, 0, 0]
-        ]
-      },
-     "Pig":{
-       "original name":"Pig",
-       "Nucleotide GTR":0.187244836750842,
-       "Global MG94xREV":0.1925639552436359,
-       "codon":[
-        ["---", "---", "---", "---", "---", "ACT", "GAG", "GTT", "GTC", "TGG", "GGC", "ATC", "GTG", "GAT", "CAA", "GAC", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GAA", "CTT", "TCA", "AAA", "CAT", "GAT", "AAC", "GTA", "GAT", "CAT", "ATA", "CGA", "TGG", "CAG", "AAG", "---", "---", "AAT", "GAA", "AAC", "AAG", "ATC", "GCA", "GAA", "TTT", "AAA", "AAA", "AAC", "AAA", "GAA", "ACT", "CAC", "CCT", "GTG", "AAA", "GAC", "ACA", "TAC", "ATG", "ATG", "TTA", "CCA", "AAT", "GGA", "ACT", "CTG", "AGA", "ATT", "AAA", "GAT", "---", "CTG", "AAG", "AGA", "GAT", "GAT", "GAG", "GGT", "ATC", "TAC", "AAG", "GTA", "ACT", "GTC", "TAT", "GCT", "ACG", "GAT", "GGA", "AAA", "CAC", "ATG", "CTG", "GAG", "AGA", "AAA", "TTT", "GAT", "TTG", "CCG", "ATT", "CTA", "GAT", "GGG", "GTC", "TCA", "AAA", "CCT", "GTA", "ATC", "TCC", "TGG", "AGC", "TGT", "GCC", "GAC", "AAA", "ACG", "GTG", "ACC", "TGT", "GAG", "GTA", "GCA", "GAA", "GGA", "AGT", "GAC", "CCT", "AAG", "TTA", "AAA", "CTG", "TAT", "GTA", "AAT", "AAG", "TCC", "ACT", "GCC", "AGA", "GAA", "GGT", "CGT", "CAG", "AAG", "GTC", "ATC", "CTG", "TGG", "AAG", "TGG", "AAC", "ACC", "AAA", "TGG", "AGC", "ACA", "TTA", "TTC", "AAG", "TGT", "GTG", "GCC", "AGT", "AAC", "AAC", "GCC", "AGT", "GAG", "CAA", "ATC", "AGC", "ATG", "GTG", "ACC", "ATC", "AGT", "TGT", "ACG", "GGG", "CAA", "GGT", "CTG", "GAT"]
-        ],
-       "amino-acid":[
-        ["-", "-", "-", "-", "-", "T", "E", "V", "V", "W", "G", "I", "V", "D", "Q", "D", "I", "N", "L", "D", "I", "P", "E", "L", "S", "K", "H", "D", "N", "V", "D", "H", "I", "R", "W", "Q", "K", "-", "-", "N", "E", "N", "K", "I", "A", "E", "F", "K", "K", "N", "K", "E", "T", "H", "P", "V", "K", "D", "T", "Y", "M", "M", "L", "P", "N", "G", "T", "L", "R", "I", "K", "D", "-", "L", "K", "R", "D", "D", "E", "G", "I", "Y", "K", "V", "T", "V", "Y", "A", "T", "D", "G", "K", "H", "M", "L", "E", "R", "K", "F", "D", "L", "P", "I", "L", "D", "G", "V", "S", "K", "P", "V", "I", "S", "W", "S", "C", "A", "D", "K", "T", "V", "T", "C", "E", "V", "A", "E", "G", "S", "D", "P", "K", "L", "K", "L", "Y", "V", "N", "K", "S", "T", "A", "R", "E", "G", "R", "Q", "K", "V", "I", "L", "W", "K", "W", "N", "T", "K", "W", "S", "T", "L", "F", "K", "C", "V", "A", "S", "N", "N", "A", "S", "E", "Q", "I", "S", "M", "V", "T", "I", "S", "C", "T", "G", "Q", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.8333333333333334, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 2, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 2, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 2, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 2, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 2.166666666666667, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0]
-        ]
-      },
-     "Horse":{
-       "original name":"Horse",
-       "Nucleotide GTR":0.2091766851769093,
-       "Global MG94xREV":0.2110982429975043,
-       "codon":[
-        ["---", "---", "---", "---", "AAG", "AAT", "ATC", "ACC", "ATC", "TTG", "GGT", "GCC", "CTG", "GAA", "CGT", "GAT", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GCT", "TTT", "CAA", "ATG", "AGT", "GAG", "CAT", "GTA", "GAA", "GAT", "ATA", "CAA", "TGG", "AGC", "AAA", "---", "---", "GGA", "AAA", "ACC", "AAG", "ATT", "GCA", "AAA", "TTC", "AAA", "AAT", "GGC", "AGT", "ATG", "ACT", "TTC", "CAG", "AAA", "GAT", "AAA", "ACA", "TAC", "GAG", "GTA", "TTA", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "CAT", "---", "CTG", "GAG", "AGA", "ATT", "CAT", "GAA", "GGT", "ACC", "TAC", "AAG", "GTA", "GAC", "GCA", "TAT", "GAT", "AGT", "GAT", "GGA", "AAA", "AAT", "GTG", "TTG", "GAG", "GAA", "ACA", "TTT", "CAT", "TTG", "AGC", "CTT", "CTA", "GAG", "ATG", "GTC", "TCA", "AAA", "CCT", "AAT", "ATC", "TCC", "TGG", "AGC", "TGC", "ACC", "AAC", "ACC", "ACC", "CTG", "ACC", "TGC", "GAG", "GTG", "ACA", "AAA", "GGA", "ACT", "GAC", "TTT", "GAG", "TTA", "AAA", "CTC", "TAT", "CTA", "AAT", "GGG", "AGA", "ATG", "ATC", "CAA", "AAA", "AGT", "CCT", "CGC", "AAA", "GTC", "ATC", "GTA", "TAC", "AAG", "CGG", "GCC", "AGC", "AAC", "CAA", "ATT", "GCG", "TCC", "TTC", "AAG", "TGC", "ACA", "GCC", "AAT", "AAC", "ACA", "GTC", "AGC", "GAG", "GAA", "AGC", "AGC", "TCT", "GTG", "GTC", "ATC", "AGG", "TGT", "ACA", "GAG", "AAA", "GGT", "CTG", "GAT"]
-        ],
-       "amino-acid":[
-        ["-", "-", "-", "-", "K", "N", "I", "T", "I", "L", "G", "A", "L", "E", "R", "D", "I", "N", "L", "D", "I", "P", "A", "F", "Q", "M", "S", "E", "H", "V", "E", "D", "I", "Q", "W", "S", "K", "-", "-", "G", "K", "T", "K", "I", "A", "K", "F", "K", "N", "G", "S", "M", "T", "F", "Q", "K", "D", "K", "T", "Y", "E", "V", "L", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "E", "R", "I", "H", "E", "G", "T", "Y", "K", "V", "D", "A", "Y", "D", "S", "D", "G", "K", "N", "V", "L", "E", "E", "T", "F", "H", "L", "S", "L", "L", "E", "M", "V", "S", "K", "P", "N", "I", "S", "W", "S", "C", "T", "N", "T", "T", "L", "T", "C", "E", "V", "T", "K", "G", "T", "D", "F", "E", "L", "K", "L", "Y", "L", "N", "G", "R", "M", "I", "Q", "K", "S", "P", "R", "K", "V", "I", "V", "Y", "K", "R", "A", "S", "N", "Q", "I", "A", "S", "F", "K", "C", "T", "A", "N", "N", "T", "V", "S", "E", "E", "S", "S", "S", "V", "V", "I", "R", "C", "T", "E", "K", "G", "L", "D"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0.5, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.1666666666666667, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 1, 0, 1.5, 1, 1, 1, 0, 0, 0, 1.5, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 2.833333333333333, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 2, 1, 1, 0, 1, 1, 2, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 2, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 1, 1, 1, 0, 1.5, 0, 0, 0, 2, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 1, 0, 0, 0, 2.5, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0]
-        ]
-      },
-     "Cat":{
-       "original name":"Cat",
-       "Nucleotide GTR":0.266381043956941,
-       "Global MG94xREV":0.2737764366992667,
-       "codon":[
-        ["---", "---", "---", "GCA", "AAT", "GAT", "GAT", "ATC", "GTC", "TGG", "GGT", "ACC", "CTG", "GGT", "CAG", "GAC", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GAT", "TCT", "CAA", "---", "GGG", "ATT", "AAT", "ATA", "GAT", "GAT", "ATA", "CAC", "TGG", "GAA", "AAA", "---", "---", "GGC", "AAG", "AAG", "AAG", "GTG", "GCG", "AGG", "TTC", "CAA", "ATT", "AGC", "AAC", "AAG", "CCT", "AAG", "AAT", "CCA", "GAT", "GAA", "AAA", "TAT", "AAT", "GTG", "TCA", "ATG", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "CAT", "---", "CTG", "ATG", "CTA", "GAA", "GAC", "TGC", "GAT", "ACC", "TAC", "AAG", "GTT", "GTT", "ATA", "TAC", "GAT", "AAG", "GAT", "GGA", "AAG", "AAT", "GTG", "TTG", "GAT", "AAA", "ACA", "TTT", "CAG", "CTG", "AAG", "ATT", "CAA", "GAG", "AAG", "GTC", "TCA", "ACG", "CCT", "AAC", "ATC", "GAC", "TGG", "AAT", "TGT", "ATC", "AAC", "AAA", "ACC", "CTG", "GTC", "TGT", "AAG", "GTA", "TCA", "AAT", "GGA", "ACA", "GAC", "CCT", "GAA", "TTA", "AAA", "CTG", "TAC", "GTA", "AAT", "GGG", "ACC", "AGT", "ATC", "AAG", "CCC", "GTT", "TCT", "TCG", "AAG", "TTC", "AGC", "ACA", "TAC", "AGG", "TTT", "ATA", "AAC", "AAG", "CAG", "AAG", "ATA", "TTA", "GTC", "AAC", "TGC", "ACG", "GCA", "GAA", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "AGC", "GAC", "GTG", "AAG", "ATG", "ATC", "ACT", "TGT", "TCA", "GAG", "AAG", "GGT", "CTG", "GAC"]
-        ],
-       "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"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0.5, 1, 1.5, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 1, 0.5, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 1, 0, 1, 1.5, 2, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1.5, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1.5, 0, 1.5, 0, 1, 1.5, 2, 1, 0, 0, 3, 1, 2, 2, 0, 1, 0, 1, 0, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1.5, 1, 0, 1.5, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 2, 0, 1, 0, 1, 0, 1, 0, 0, 2, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1.5, 1, 1, 2, 0, 1, 1, 0, 0, 1, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 0, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 2, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0]
-        ]
-      },
-     "Mouse":{
-       "original name":"Mouse",
-       "Nucleotide GTR":0.1181831744338598,
-       "Global MG94xREV":0.1201249221156985,
-       "codon":[
-        ["---", "---", "---", "AGA", "GAC", "AAT", "GAG", "ACC", "ATC", "TGG", "GGT", "GTC", "TTG", "GGT", "CAT", "GGC", "ATC", "ACC", "CTG", "AAC", "ATC", "CCC", "AAC", "TTT", "CAA", "ATG", "ACT", "GAT", "GAT", "ATT", "GAT", "GAG", "GTG", "CGA", "TGG", "GTA", "AGG", "---", "---", "AGG", "GGC", "ACC", "CTG", "GTC", "GCA", "GAG", "TTT", "AAA", "AGG", "AAG", "AAG", "CCA", "CCT", "TTT", "TTG", "ATA", "TCA", "GAA", "ACG", "TAT", "GAG", "GTC", "TTA", "GCA", "AAC", "GGA", "TCC", "CTG", "AAG", "ATA", "AAG", "AAG", "CCG", "ATG", "ATG", "AGA", "AAC", "GAC", "AGT", "GGC", "ACC", "TAT", "AAT", "GTA", "ATG", "GTG", "TAT", "GGC", "ACA", "AAT", "GGG", "ATG", "ACT", "AGG", "CTG", "GAG", "AAG", "GAC", "CTG", "GAC", "GTG", "AGG", "ATT", "CTG", "GAG", "AGG", "GTC", "TCA", "AAG", "CCC", "ATG", "ATC", "CAC", "TGG", "GAA", "TGC", "CCC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GCG", "GTC", "TTG", "CAA", "GGG", "ACA", "GAT", "TTT", "GAA", "CTG", "AAG", "CTG", "TAT", "CAA", "GGG", "GAA", "ACA", "CTA", "CTC", "AAT", "AGT", "CTC", "CCC", "CAG", "AAG", "AAC", "ATG", "AGT", "TAC", "CAG", "TGG", "---", "ACC", "AAC", "CTG", "AAC", "GCA", "CCA", "TTC", "AAG", "TGT", "GAG", "GCG", "ATA", "AAC", "CCG", "GTC", "AGC", "AAG", "GAG", "TCT", "AAG", "ATG", "GAA", "GTT", "GTT", "AAC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "TCC"]
-        ],
-       "amino-acid":[
-        ["-", "-", "-", "R", "D", "N", "E", "T", "I", "W", "G", "V", "L", "G", "H", "G", "I", "T", "L", "N", "I", "P", "N", "F", "Q", "M", "T", "D", "D", "I", "D", "E", "V", "R", "W", "V", "R", "-", "-", "R", "G", "T", "L", "V", "A", "E", "F", "K", "R", "K", "K", "P", "P", "F", "L", "I", "S", "E", "T", "Y", "E", "V", "L", "A", "N", "G", "S", "L", "K", "I", "K", "K", "P", "M", "M", "R", "N", "D", "S", "G", "T", "Y", "N", "V", "M", "V", "Y", "G", "T", "N", "G", "M", "T", "R", "L", "E", "K", "D", "L", "D", "V", "R", "I", "L", "E", "R", "V", "S", "K", "P", "M", "I", "H", "W", "E", "C", "P", "N", "T", "T", "L", "T", "C", "A", "V", "L", "Q", "G", "T", "D", "F", "E", "L", "K", "L", "Y", "Q", "G", "E", "T", "L", "L", "N", "S", "L", "P", "Q", "K", "N", "M", "S", "Y", "Q", "W", "-", "T", "N", "L", "N", "A", "P", "F", "K", "C", "E", "A", "I", "N", "P", "V", "S", "K", "E", "S", "K", "M", "E", "V", "V", "N", "C", "P", "E", "K", "G", "L", "S"]
-        ],
-       "synonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0.5, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0]
-        ],
-       "nonsynonymous substitution count":[
-        [0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1.5, 1, 1, 0, 0, 0, 1.5, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.5, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1]
-        ]
-      },
-     "Rat":{
-       "original name":"Rat",
-       "Nucleotide GTR":0.06669700444436912,
-       "Global MG94xREV":0.06710985342857588,
-       "codon":[
-        ["---", "---", "---", "AGA", "GAC", "AGT", "GGG", "ACC", "GTC", "TGG", "GGT", "GCC", "CTG", "GGT", "CAT", "GGC", "ATC", "AAC", "CTG", "AAC", "ATC", "CCT", "AAC", "TTT", "CAA", "ATG", "ACT", "GAT", "GAT", "ATT", "GAT", "GAG", "GTG", "CGA", "TGG", "GAG", "AGG", "---", "---", "GGG", "AGC", "ACC", "CTG", "GTT", "GCC", "GAG", "TTT", "AAA", "AGG", "AAG", "ATG", "AAG", "CCT", "TTT", "TTG", "AAA", "TCG", "GGA", "GCA", "TTT", "GAG", "ATC", "TTA", "GCA", "AAT", "GGA", "GAC", "TTG", "AAG", "ATA", "AAG", "AAT", "---", "CTG", "ACA", "AGA", "GAT", "GAC", "AGT", "GGC", "ACC", "TAT", "AAT", "GTA", "ACG", "GTA", "TAC", "AGC", "ACA", "AAT", "GGG", "ACA", "CGT", "ATC", "CTG", "GAC", "AAG", "GCA", "CTG", "GAC", "TTG", "AGG", "ATT", "CTA", "GAG", "ATG", "GTC", "TCA", "AAG", "CCG", "ATG", "ATC", "TAC", "TGG", "GAG", "TGC", "AGC", "AAC", "GCA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTC", "TTG", "GAA", "GGA", "ACA", "GAT", "GTT", "GAA", "CTA", "AAG", "CTG", "TAC", "CAA", "GGA", "AAG", "GAG", "CAT", "CTC", "AGG", "AGC", "CTC", "CGT", "CAG", "AAG", "ACC", "ATG", "AGT", "TAC", "CAG", "TGG", "---", "ACC", "AAC", "CTG", "AGA", "GCA", "CCG", "TTT", "AAG", "TGC", "AAG", "GCG", "GTA", "AAC", "AGG", "GTC", "AGC", "CAG", "GAG", "TCT", "GAG", "ATG", "GAA", "GTT", "GTC", "AAC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "CCC"]
-        ],
-       "amino-acid":[
-        ["-", "-", "-", "R", "D", "S", "G", "T", "V", "W", "G", "A", "L", "G", "H", "G", "I", "N", "L", "N", "I", "P", "N", "F", "Q", "M", "T", "D", "D", "I", "D", "E", "V", "R", "W", "E", "R", "-", "-", "G", "S", "T", "L", "V", "A", "E", "F", "K", "R", "K", "M", "K", "P", "F", "L", "K", "S", "G", "A", "F", "E", "I", "L", "A", "N", "G", "D", "L", "K", "I", "K", "N", "-", "L", "T", "R", "D", "D", "S", "G", "T", "Y", "N", "V", "T", "V", "Y", "S", "T", "N", "G", "T", "R", "I", "L", "D", "K", "A", "L", "D", "L", "R", "I", "L", "E", "M", "V", "S", "K", "P", "M", "I", "Y", "W", "E", "C", "S", "N", "A", "T", "L", "T", "C", "E", "V", "L", "E", "G", "T", "D", "V", "E", "L", "K", "L", "Y", "Q", "G", "K", "E", "H", "L", "R", "S", "L", "R", "Q", "K", "T", "M", "S", "Y", "Q", "W", "-", "T", "N", "L", "R", "A", "P", "F", "K", "C", "K", "A", "V", "N", "R", "V", "S", "Q", "E", "S", "E", "M", "E", "V", "V", "N", "C", "P", "E", "K", "G", "L", "P"]
-        ],
-       "synonymous substitution count":[
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-     "Nucleotide GTR":{
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-       "display order":0
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-     "Global MG94xREV":{
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-     "codon":{
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-     "synonymous substitution count":{
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  "MLE":{
-   "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 P<sub>s</sub> probability of success"],
-    ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with P<sub>s</sub> probability of success"],
-    ["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"]
-    ],
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           ]
         }
       }
+    },
+   "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 P<sub>s</sub> probability of success"],
+    ["P [dN/dS < 1]", "Binomial probability that S is no less than the observed value, with P<sub>s</sub> 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", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "R", "M", "E", "T", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
+        ],
+       "codon":        [
+["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AAA", "TGG", "GAG", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ],
+       "original name":"Baboon",
+       "synonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ]
+      },
+     "Cat":{
+       "Global MG94xREV":0.270986057489719,
+       "Nucleotide 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":        [
+["---", "---", "---", "GCA", "AAT", "GAT", "GAT", "ATC", "GTC", "TGG", "GGT", "ACC", "CTG", "GGT", "CAG", "GAC", "ATC", "AAC", "CTG", "GAC", "ATT", "CCT", "GAT", "TCT", "CAA", "---", "GGG", "ATT", "AAT", "ATA", "GAT", "GAT", "ATA", "CAC", "TGG", "GAA", "AAA", "---", "---", "GGC", "AAG", "AAG", "AAG", "GTG", "GCG", "AGG", "TTC", "CAA", "ATT", "AGC", "AAC", "AAG", "CCT", "AAG", "AAT", "CCA", "GAT", "GAA", "AAA", "TAT", "AAT", "GTG", "TCA", "ATG", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "CAT", "---", "CTG", "ATG", "CTA", "GAA", "GAC", "TGC", "GAT", "ACC", "TAC", "AAG", "GTT", "GTT", "ATA", "TAC", "GAT", "AAG", "GAT", "GGA", "AAG", "AAT", "GTG", "TTG", "GAT", "AAA", "ACA", "TTT", "CAG", "CTG", "AAG", "ATT", "CAA", "GAG", "AAG", "GTC", "TCA", "ACG", "CCT", "AAC", "ATC", "GAC", "TGG", "AAT", "TGT", "ATC", "AAC", "AAA", "ACC", "CTG", "GTC", "TGT", "AAG", "GTA", "TCA", "AAT", "GGA", "ACA", "GAC", "CCT", "GAA", "TTA", "AAA", "CTG", "TAC", "GTA", "AAT", "GGG", "ACC", "AGT", "ATC", "AAG", "CCC", "GTT", "TCT", "TCG", "AAG", "TTC", "AGC", "ACA", "TAC", "AGG", "TTT", "ATA", "AAC", "AAG", "CAG", "AAG", "ATA", "TTA", "GTC", "AAC", "TGC", "ACG", "GCA", "GAA", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "AGC", "GAC", "GTG", "AAG", "ATG", "ATC", "ACT", "TGT", "TCA", "GAG", "AAG", "GGT", "CTG", "GAC"] 
+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 1, 0, 1, 1.5, 2, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1.5, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1.5, 0, 1.5, 0, 1, 1.5, 2, 1, 0, 0, 3, 1, 2, 2, 0, 1, 0, 1, 0, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1.5, 1, 0, 1.5, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 2, 0, 1, 0, 1, 0, 1, 0, 0, 2, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1.5, 1, 1, 2, 0, 1, 1, 0, 0, 1, 2, 1, 1, 1, 1, 2, 2, 1, 1, 1, 0, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 2, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0] 
+        ],
+       "original name":"Cat",
+       "synonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0.5, 1, 1.5, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 1, 0.5, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0] 
+        ]
+      },
+     "Chimp":{
+       "Global MG94xREV":0.001852173963769908,
+       "Nucleotide GTR":0.001818397708700883,
+       "amino-acid":        [
+["E", "E", "I", "T", "N", "A", "L", "E", "T", "W", "G", "A", "L", "G", "Q", "D", "I", "N", "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", "K", "E", "K", "D", "T", "Y", "K", "L", "F", "K", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "T", "D", "D", "Q", "D", "I", "Y", "K", "V", "S", "I", "Y", "D", "T", "K", "G", "K", "N", "V", "L", "E", "K", "I", "F", "D", "L", "K", "I", "Q", "E", "R", "V", "S", "K", "P", "K", "I", "S", "W", "T", "C", "I", "N", "T", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "D", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "L", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "S", "V", "E", "P", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
+        ],
+       "codon":        [
+["GAA", "GAG", "ATT", "ACG", "AAT", "GCC", "TTG", "GAA", "ACC", "TGG", "GGT", "GCC", "TTG", "GGT", "CAG", "GAC", "ATC", "AAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAC", "GAT", "ATA", "AAA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAA", "GAG", "ACT", "TTC", "AAG", "GAA", "AAA", "GAT", "ACA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAG", "CAT", "---", "CTG", "AAG", "ACC", "GAT", "GAT", "CAG", "GAT", "ATC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAT", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ATA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "AAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTA", "ATG", "AAT", "GGA", "ACT", "GAC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "CTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCA", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGT", "GTC", "GAG", "CCT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
+        ],
+       "nonsynonymous substitution count":        [
+[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ],
+       "original name":"Chimp",
+       "synonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ]
+      },
+     "Cow":{
+       "Global MG94xREV":0.2526189686412594,
+       "Nucleotide GTR":0.2480122076744146,
+       "amino-acid":        [
+["-", "-", "-", "-", "E", "S", "I", "V", "V", "W", "G", "A", "L", "D", "H", "D", "L", "N", "L", "D", "I", "P", "G", "F", "P", "R", "S", "D", "I", "V", "A", "D", "I", "K", "W", "N", "R", "-", "-", "N", "K", "N", "K", "I", "A", "R", "I", "K", "K", "D", "M", "P", "L", "H", "N", "E", "M", "D", "K", "Y", "D", "M", "F", "T", "N", "G", "T", "L", "K", "I", "K", "T", "-", "L", "M", "R", "N", "D", "S", "G", "L", "Y", "E", "V", "E", "V", "Y", "D", "S", "N", "G", "V", "N", "L", "L", "S", "K", "K", "F", "D", "L", "K", "I", "Q", "E", "M", "L", "S", "G", "P", "E", "I", "N", "W", "I", "C", "T", "N", "R", "T", "V", "S", "C", "K", "V", "E", "N", "G", "S", "N", "P", "K", "L", "Q", "L", "F", "L", "N", "T", "T", "R", "V", "K", "Q", "D", "H", "G", "K", "L", "I", "T", "Y", "T", "W", "N", "T", "R", "W", "N", "K", "T", "F", "K", "C", "V", "A", "S", "N", "H", "V", "D", "S", "K", "V", "S", "I", "E", "I", "A", "V", "C", "P", "D", "E", "G", "L", "D"] 
+        ],
+       "codon":        [
+["---", "---", "---", "---", "GAA", "AGC", "ATT", "GTC", "GTC", "TGG", "GGT", "GCC", "CTG", "GAT", "CAT", "GAC", "CTC", "AAC", "CTG", "GAC", "ATT", "CCT", "GGT", "TTT", "CCA", "AGA", "AGT", "GAT", "ATA", "GTG", "GCA", "GAT", "ATA", "AAA", "TGG", "AAC", "AGA", "---", "---", "AAC", "AAA", "AAC", "AAG", "ATT", "GCA", "CGA", "ATA", "AAG", "AAA", "GAT", "ATG", "CCA", "CTT", "CAC", "AAT", "GAA", "ATG", "GAC", "AAA", "TAT", "GAT", "ATG", "TTT", "ACA", "AAT", "GGA", "ACT", "CTG", "AAA", "ATT", "AAA", "ACT", "---", "CTG", "ATG", "AGA", "AAC", "GAT", "AGT", "GGT", "CTC", "TAT", "GAG", "GTA", "GAG", "GTT", "TAT", "GAT", "TCA", "AAT", "GGA", "GTA", "AAC", "CTA", "CTG", "AGC", "AAA", "AAA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "ATG", "CTC", "TCA", "GGA", "CCT", "GAA", "ATT", "AAC", "TGG", "ATC", "TGT", "ACC", "AAC", "AGA", "ACT", "GTG", "AGC", "TGC", "AAG", "GTA", "GAA", "AAT", "GGA", "AGT", "AAT", "CCT", "AAA", "TTA", "CAA", "CTG", "TTT", "TTA", "AAT", "ACG", "ACC", "CGT", "GTC", "AAA", "CAA", "GAT", "CAT", "GGG", "AAG", "CTC", "ATC", "ACC", "TAC", "ACG", "TGG", "AAC", "ACC", "AGA", "TGG", "AAT", "AAA", "ACA", "TTC", "AAG", "TGC", "GTG", "GCG", "AGT", "AAC", "CAT", "GTC", "GAT", "AGC", "AAA", "GTC", "AGC", "ATA", "GAG", "ATC", "GCC", "GTG", "TGT", "CCA", "GAT", "GAA", "GGT", "CTG", "GAT"] 
+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 0, 2, 1, 1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1.5, 0, 1.5, 0, 0, 1, 0, 2, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1.5, 0, 0, 0, 1, 2, 1, 0, 0, 0, 1.5, 0, 1, 0, 2, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 1, 0, 1, 0, 1.5, 0, 1, 0, 1, 0, 1.5, 0, 0, 0, 1, 1, 0, 2, 0, 1, 0, 2.833333333333333, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 2, 0, 0, 0, 2, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 2, 1, 1, 0, 1, 0, 0, 2, 2.5, 0, 0, 1, 1, 0, 0, 0] 
+        ],
+       "original name":"Cow",
+       "synonymous substitution count":        [
+[0, 0, 0, 0, 0, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.5, 0, 0, 1, 0, 0, 0.5, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0.1666666666666667, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5, 0, 0, 0, 0, 0, 0, 0] 
+        ]
+      },
+     "Horse":{
+       "Global MG94xREV":0.2128981270938909,
+       "Nucleotide GTR":0.209015715622236,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 0, 1, 0, 1.5, 1, 1, 1, 0, 0, 0, 1.5, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 2.833333333333333, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 2, 1, 1, 0, 1, 1, 2, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1.5, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 2, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 1, 1, 1, 0, 1.5, 0, 0, 0, 2, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 0, 1, 0, 0, 0, 2.5, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0] 
+        ],
+       "original name":"Horse",
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Human":{
+       "Global MG94xREV":0,
+       "Nucleotide GTR":0,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
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+        ],
+       "original name":"Human",
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Mouse":{
+       "Global MG94xREV":0.1202934609265267,
+       "Nucleotide GTR":0.1180997886803625,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
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+        ],
+       "original name":"Mouse",
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Node1":{
+       "Global MG94xREV":0.28199060274564,
+       "Nucleotide GTR":0.2768482204901319,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1.5, 1, 0, 0, 1, 0, 0, 0, 2, 1, 2, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 2, 1, 2, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1.5, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 2.833333333333333, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 1.5, 1, 0, 0, 0, 0, 2.666666666666667, 0, 0, 0, 0, 2, 1, 1.5, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 2] 
+        ],
+       "synonymous substitution count":        [
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+        ],
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+        ]
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+        ],
+       "nonsynonymous substitution count":        [
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+        ],
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Node8":{
+       "Global MG94xREV":0.1081901197733327,
+       "Nucleotide GTR":0.106217164126135,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
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+        ],
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Node9":{
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+       "Nucleotide GTR":0.02565258733434138,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
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+        ],
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Pig":{
+       "Global MG94xREV":0.190671339253091,
+       "Nucleotide GTR":0.1871942556124935,
+       "amino-acid":        [
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+        ],
+       "codon":        [
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+        ],
+       "nonsynonymous substitution count":        [
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+        ],
+       "original name":"Pig",
+       "synonymous substitution count":        [
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+        ]
+      },
+     "Rat":{
+       "Global MG94xREV":0.06785010407729926,
+       "Nucleotide GTR":0.06661278918863184,
+       "amino-acid":        [
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+        ],
+       "codon":        [
+["---", "---", "---", "AGA", "GAC", "AGT", "GGG", "ACC", "GTC", "TGG", "GGT", "GCC", "CTG", "GGT", "CAT", "GGC", "ATC", "AAC", "CTG", "AAC", "ATC", "CCT", "AAC", "TTT", "CAA", "ATG", "ACT", "GAT", "GAT", "ATT", "GAT", "GAG", "GTG", "CGA", "TGG", "GAG", "AGG", "---", "---", "GGG", "AGC", "ACC", "CTG", "GTT", "GCC", "GAG", "TTT", "AAA", "AGG", "AAG", "ATG", "AAG", "CCT", "TTT", "TTG", "AAA", "TCG", "GGA", "GCA", "TTT", "GAG", "ATC", "TTA", "GCA", "AAT", "GGA", "GAC", "TTG", "AAG", "ATA", "AAG", "AAT", "---", "CTG", "ACA", "AGA", "GAT", "GAC", "AGT", "GGC", "ACC", "TAT", "AAT", "GTA", "ACG", "GTA", "TAC", "AGC", "ACA", "AAT", "GGG", "ACA", "CGT", "ATC", "CTG", "GAC", "AAG", "GCA", "CTG", "GAC", "TTG", "AGG", "ATT", "CTA", "GAG", "ATG", "GTC", "TCA", "AAG", "CCG", "ATG", "ATC", "TAC", "TGG", "GAG", "TGC", "AGC", "AAC", "GCA", "ACC", "CTG", "ACC", "TGT", "GAG", "GTC", "TTG", "GAA", "GGA", "ACA", "GAT", "GTT", "GAA", "CTA", "AAG", "CTG", "TAC", "CAA", "GGA", "AAG", "GAG", "CAT", "CTC", "AGG", "AGC", "CTC", "CGT", "CAG", "AAG", "ACC", "ATG", "AGT", "TAC", "CAG", "TGG", "---", "ACC", "AAC", "CTG", "AGA", "GCA", "CCG", "TTT", "AAG", "TGC", "AAG", "GCG", "GTA", "AAC", "AGG", "GTC", "AGC", "CAG", "GAG", "TCT", "GAG", "ATG", "GAA", "GTT", "GTC", "AAC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "CCC"] 
+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ],
+       "original name":"Rat",
+       "synonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ]
+      },
+     "RhMonkey":{
+       "Global MG94xREV":0.003845100000905624,
+       "Nucleotide GTR":0.003774980735147155,
+       "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", "R", "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", "TI", "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", "T", "L", "T", "C", "E", "V", "M", "N", "G", "T", "DG", "P", "E", "L", "N", "L", "Y", "Q", "D", "G", "K", "H", "V", "K", "-", "L", "S", "Q", "R", "V", "I", "T", "H", "K", "W", "T", "T", "S", "L", "S", "A", "K", "F", "K", "C", "T", "A", "G", "N", "K", "V", "S", "K", "E", "S", "R", "M", "E", "T", "V", "S", "C", "P", "E", "K", "G", "L", "D"] 
+        ],
+       "codon":        [
+["AAA", "GAG", "ATT", "AGG", "AAT", "GCT", "TTG", "GAA", "ACC", "TGG", "GGA", "GCG", "CTG", "GGT", "CAG", "GAC", "ATC", "GAC", "TTG", "GAC", "ATT", "CCT", "AGT", "TTT", "CAA", "ATG", "AGT", "GAT", "GAT", "ATT", "GAT", "GAT", "ATA", "AGA", "TGG", "GAA", "AAA", "ACT", "TCA", "GAC", "AAG", "AAA", "AAG", "ATT", "GCA", "CAA", "TTC", "AGA", "AAA", "GAG", "AAG", "GAG", "ACT", "TTC", "GAG", "GAA", "AAA", "GAT", "GCA", "TAT", "AAG", "CTA", "TTT", "AAA", "AAC", "GGA", "ACT", "CTG", "AAA", "AYT", "AAG", "CAT", "---", "CTG", "AAG", "ATC", "CAT", "GAT", "CAG", "GAT", "AGC", "TAC", "AAG", "GTA", "TCA", "ATA", "TAC", "GAT", "ACA", "AAA", "GGA", "AAA", "AAT", "GTG", "TTG", "GAA", "AAA", "ACA", "TTT", "GAT", "TTG", "AAG", "ATT", "CAA", "GAG", "AGG", "GTC", "TCA", "GAA", "CCA", "AAG", "ATC", "TCC", "TGG", "ACT", "TGT", "ATC", "AAC", "ACA", "ACC", "CTG", "ACC", "TGT", "GAA", "GTA", "ATG", "AAT", "GGA", "ACT", "GRC", "CCC", "GAA", "TTA", "AAC", "CTG", "TAT", "CAA", "GAT", "GGG", "AAA", "CAT", "GTA", "AAA", "---", "CTT", "TCT", "CAG", "AGG", "GTC", "ATC", "ACA", "CAC", "AAG", "TGG", "ACC", "ACC", "AGC", "CTG", "AGT", "GCG", "AAA", "TTC", "AAG", "TGC", "ACA", "GCA", "GGG", "AAC", "AAA", "GTC", "AGC", "AAG", "GAA", "TCC", "AGG", "ATG", "GAG", "ACT", "GTC", "AGC", "TGT", "CCA", "GAG", "AAA", "GGT", "CTG", "GAC"] 
+        ],
+       "nonsynonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ],
+       "original name":"RhMonkey",
+       "synonymous substitution count":        [
+[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] 
+        ]
+      }
+    },
+   "attributes":{
+     "Global MG94xREV":{
+       "attribute type":"branch length",
+       "display order":1
+      },
+     "Nucleotide GTR":{
+       "attribute type":"branch length",
+       "display order":0
+      },
+     "amino-acid":{
+       "attribute type":"node label",
+       "display order":1
+      },
+     "codon":{
+       "attribute type":"node label",
+       "display order":0
+      },
+     "nonsynonymous substitution count":{
+       "attribute type":"branch label",
+       "display order":1
+      },
+     "original name":{
+       "attribute type":"node label",
+       "display order":-1
+      },
+     "synonymous substitution count":{
+       "attribute type":"branch label",
+       "display order":0
+      }
     }
   },
- "sample-median":{
+ "data partitions":{
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+     "Log Likelihood":-3467.333825435224,
+     "Rate Distributions":{
+       "non-synonymous/synonymous rate ratio for *test*":        [
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+   "Nucleotide GTR":{
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+   "number of sequences":10,
+   "number of sites":187,
+   "partition count":1,
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+      ]
+    }
+  },
+ "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