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mitochondria.dawg
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mitochondria.dawg
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# Test mitochondria root code
# Genetic codes -- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2
# 2 = The Vertevrate Mitochondrial Code
Tree.Scale = 0.99999
Root.Length = 100
Root.Code = 2
Root.Seq = "ACTTTGAATGGGATATTTTCATACACACCGTCTTTGAAGTGTACTGACCTCTTCATGATAATAGGTCTGGTCATGATATGCTACTTCTCTTAGCTGTCGTTCTAATCATCTGTTGGCACAACATTGCGTAATGGAAATGGATAACTTTTCTGTTTAGTTTGCTCTGTGGCTCTATCTAGAAAATTAAAGGATACAAAACTAATTAACCATTCTTATAAATCACTAAGCCAGCACAATGGTTTCTACTGCTGTCAGCCTTTATTTTCAATTTTTCTTAGTCCCCTAGCTTTTCCGTAAACACCGAACACTTCTCTCGTATGATTGGTGCAAACCGTTTGGTGAAAAAAAGCACATTTGCATATACAAAAAATTAACAAATCTATCATATAATAATTAAGATATAGAGTTCATGATCCTTGTGCCATTGATCAAGCCATCGGCGATGATGATAAACCTTTTATTGATACCTTTTTTACCTAGTATTTTTTGCAAATGCTTCATTGTTACACCTCCGAGGAATACTACGAGTGCAATATCCTCTGCAGCATGAAATGTCCCATTAGATCCGTCTATGGACCGTCTATTATTGCTCTTGATGCTTGCATTGATCTTTTTTGTAATGGTTCCCGGGACCCATATACTCTCTTCGATCGCATGTGAGTCTCCATATAACTGTTCAATTAAATCCTCCGTTTGAGAAACTCTAGGTTCTCTTGACAGTATAAAAGGCTGCTGCGAGGAATAATTATGGAACAAGATAGACCTATCATATAACATCTGAACCAGTCTCATTGTCAAGGGCACTACACCACTGTAAGCAAAAGTGGCTTCCGAGAAGTCATCGTTCTCATTTGTGATTTTATCGGCAGCATGCTCGTCTTCTATGGGTACTGTATTGAACCATTGTGAAATATAACGGTATTCTTTCTGTAATCTTGTTGACTTACTTGTTGTAATATGCAAATCAGTTTTTCCCGTTTTGCTAGTGAAAAATCCTAAGCCAATGATTCAAGTTGAAAGCATTTTTCAATGCCCCAAGAGTCGATCATAAAGGTTCTTAGATATTCATAATCCTTTTCTCGAAGTGAATTTTTACAAAGAGACAATAAACAGATTAATCTGAGAATCTTCTTTTGATCAACCTCGTACTGGTACTGCAACTCGAGTATAATATCTTCAATGTCGTTATTAAGTGTATTTCCCATCAAAATTTCCAGCTCTAACTCTAAGATTTTATTGAAAGATCCGTACTCTTCAGTCTCTACCACTTTCAAAACGTCGGATGATAAGGTTGTGTGATTTTTCAAAAAAGCTTGCCTTTGTTGCAAAGAACCTAAGGAATCAACGAATTCTTTGATTTCATGTACGCTCTCGGCTTTATGCCTTGTATCATATTGCGTTTGTAGTTCCTTTGCCAATTTATTTAACTGCGGCCCAATCGACCCAAAATTTAAAAATTTCAAATCATTCCATATTTTATCTTCCTTATAATTGAA"
Sim.Reps = 10
Sim.Seed = 42
Root.Seg = 0
[[-]]
Tree.Tree = "(D:0.3, E:0.2)C;"
Subst.Model = "gtr"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
Subst.Rate.Model = "ZERO"
Root.Seg = 1
[[-]]
Tree.Tree = "(A:0.3, B:0.2)C;"
Subst.Model = "jc"
Subst.Rate.Model = "CONST"
Root.Seg = 1
[[-]]
Tree.Tree = "(F:0.3, G:0.2)C;"
Subst.Model = "k2p"
Subst.Rate.Model = "ZERO"
Root.Seg = 3
[[-]]
Tree.Tree = "(H:0.3, I:0.2)C;"
Subst.Model = "hky"
Subst.Rate.Model = "ZERO"
Root.Seg = 2
[Indel]
Params.Ins = 1.039000, 50
Model.Ins = "GEO"
Rate.Ins = 0.01
Max.Ins = 50.0
Params.Del = 1.039000, 50
Model.Del = "POWER-LAW"
Rate.Del = 0.01
Max.Del = 50.0
[[-]]
Tree.Tree = "(J:0.3, K:0.2)C;"
Subst.Model = "f84"
Subst.Rate.Model = "ZERO"
Root.Seg = 5
[[-]]
Tree.Tree = "(L:0.3, M:0.2)C;"
Subst.Model = "f81"
Subst.Rate.Model = "ZERO"
Root.Seg = 6
[[-]]
Tree.Tree = "(N:0.3, O:0.2)C;"
Subst.Model = "tn"
Subst.Rate.Model = "ZERO"
Root.Seg = 7
[[-]]
Tree.Tree = "(P:0.3, Q:0.2)C;"
Subst.Model = "tn-f04"
Subst.Rate.Model = "ZERO"
Root.Seg = 8