Mercurial > repos > iuc > hyphy_absrel
view test-data/slac-out1.json @ 23:5a7c56a5cc08 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 05ae58b803965f16da05329ef4a84fa6434382ce"
author | iuc |
---|---|
date | Fri, 09 Apr 2021 21:51:00 +0000 |
parents | 0b58ef9e84b2 |
children |
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0.2397204872545077, 1.725289655759397] ] } } }, "headers": [ ["ES", "Expected synonymous sites"], ["EN", "Expected non-synonymous sites"], ["S", "Inferred synonymous substitutions"], ["N", "Inferred non-synonymous substitutions"], ["P[S]", "Expected proportion of synonymous sites"], ["dS", "Inferred synonymous susbsitution rate"], ["dN", "Inferred non-synonymous susbsitution rate"], ["dN-dS", "Scaled by the length of the tested branches"], ["P [dN/dS > 1]", "Binomial probability that S is no greater than the observed value, with 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", 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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": [ ["-", "-", "-", "-", "K", "N", "I", "T", "I", "L", "G", "A", "L", "E", "R", "D", "I", "N", "L", "D", "I", "P", "A", "F", "Q", "M", "S", 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GTR":0.09882578298426958, "amino-acid": [ ["-", "-", "-", "-", "N", "N", "V", "V", "V", "W", "G", "A", "L", "D", "H", "D", "I", "N", "L", "D", "I", "P", "D", "F", "P", "K", "S", "D", "N", "V", "D", "D", "I", "Q", "W", "E", "K", "-", "-", "N", "K", "N", "K", "I", "A", "Q", "F", "K", "K", "D", "K", "K", "P", "H", "N", "E", "K", "D", "T", "Y", "K", "M", "L", "T", "N", "G", "T", "L", "K", "I", "K", "H", "-", "L", "K", "R", "D", "D", "G", "G", "I", "Y", "K", "V", "A", "V", "Y", "D", "T", "D", "G", "K", "N", "V", "L", "E", "K", "K", "F", "D", "L", "K", "I", "L", "E", "R", "V", "S", "K", "P", "E", "I", "S", "W", "S", "C", "T", "N", "K", "T", "V", "T", "C", "E", "V", "A", "N", "G", "S", "D", "P", "K", "L", "K", "L", "Y", "L", "N", "R", "T", "S", "V", "K", "Q", "G", "P", "Q", "K", "V", "I", "T", "Y", "K", "W", "N", "T", "K", "W", "S", "T", "S", "F", "K", "C", "V", "A", "S", "N", "N", "V", "S", "K", "E", "I", "S", "M", "E", "I", "I", "S", "C", "P", "E", "K", "G", "L", "D"] ], "codon": [ ["---", 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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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 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, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 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, 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, 0, 0, 0, 0, 1] ] }, "Node8":{ "Global MG94xREV":0.1081901197733327, "Nucleotide GTR":0.106217164126135, "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", 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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] ] }, "Node9":{ "Global MG94xREV":0.0261290773391622, "Nucleotide GTR":0.02565258733434138, "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", 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