Skip to content
Permalink
Browse files

Update mitochondria trick to use vertebrate root code \

Add notes to error trick file \
Add sections to rna trick
  • Loading branch information...
zmertens committed Feb 9, 2018
1 parent 577b89f commit afff69beea9a1cde39931587869d4c83891633f0
Showing with 131 additions and 125 deletions.
  1. +54 −56 examples/error.dawg
  2. +41 −33 examples/mitochondria.dawg
  3. +36 −36 examples/rna.dawg
@@ -1,61 +1,59 @@
# Test mitochondria root code
# vertebrate root code -- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2
# Test using different sequence types in a single trick file
# Try to cause an error

Tree.Tree = "(A:0.3, B:0.2)C;"
Tree.Scale = 0.99999
Tree.Scale = 4.99999
Root.Length = 100
Root.Code = TCAAAAGGGGTTTTCCCCAAATTAAGGCCCC
Root.Seq = "bad root sequence"
Root.Code = 2
Root.Seq = "GHAGCVFFYTDYSIGDGFCCMVMYC"
Sim.Reps = 10
Sim.Seed = 42
Root.Seg = 0

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"

Subst.Model = "jc"
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"

Subst.Model = "f81"
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"

Subst.Model = "k2p"
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"

Subst.Model = "tn"
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"

Subst.Model = "tn_f04"
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"

Subst.Model = "f84"
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"

Subst.Model = "hky"
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"

Subst.Model = "jtt"
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"

Subst.Model = "dayhoff"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
Subst.Rate.Model = "ZERO"
Output.Markins=1

[[ProteinSequence]]
Tree.Tree = "(X:0.3, Y:0.2)Z;"
Subst.Model = "aagtr"
Subst.Freqs =
0.443, 0.3113, 0.3, 0.2, 0.888, 0.6520, 0.9112, 0.3323, 0.2998, 0.7171,
0.443, 0.3113, 0.3003, 0.211, 0.5588, 0.43520, 0.487112, 0.76323, 0.1998, 0.44171
Subst.Params =
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171,
100.443, 49.3113, 66.3, 10.2, 40.888, 3.6520, 49.9112, 22.3323, 48.2998, 33.7171
Subst.Rate.Model = "CONST"
Root.Seg = 1
Root.Code=13
[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

# [[DnaSequence]]
# Tree.Tree = "(A:0.3, B:0.2)Z;"
# 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 = 2
# Root.Code = 4
@@ -1,62 +1,70 @@
# Test mitochondria root code
# Genetic codes -- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2
# 13 = The Ascidian Mitochondrial Code
# 2 = The Vertevrate Mitochondrial Code

Tree.Tree = "(A:0.3, B:0.2)~C;"
Tree.Scale = 0.99999
Root.Length = 100
Root.Code = 13
# Root.Seq = "AATGTCTCCTA"
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.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"

Subst.Model = "f81"
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"
Subst.Rate.Model = "CONST"
Root.Seg = 1

[[-]]
Tree.Tree = "(F:0.3, G:0.2)C;"
Subst.Model = "k2p"
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"

Subst.Model = "tn"
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 = 3

Subst.Model = "tn_f04"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
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.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 = 5

Subst.Model = "hky"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(L:0.3, M:0.2)C;"
Subst.Model = "f81"
Subst.Rate.Model = "ZERO"
Root.Seg = 6

Subst.Model = "jtt"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(N:0.3, O:0.2)C;"
Subst.Model = "tn"
Subst.Rate.Model = "ZERO"
Root.Seg = 7

Subst.Model = "dayhoff"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(P:0.3, Q:0.2)C;"
Subst.Model = "tn-f04"
Subst.Rate.Model = "ZERO"
Root.Seg = 8
@@ -1,74 +1,74 @@
# Test rna evaluationary models
# Test RNA evolutionary models

Output.Rna = 1
Output.lowercase = 1
Output.markins = 1
Output.keepempty = 0
Tree.Tree = "(A:0.3, B:0.2)C;"
Tree.Tree = "(X:0.3, Y:0.2)D;"
Tree.Scale = 0.99999
Root.Length = 100
Root.Code = 2
Root.Seq = "ACGTACGT"
Root.Seq = "ACGTACGTTTAAAATTAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTTTTGGGGGGGGGGGGGGGCCCCCCCCCCCCAATTA"
Sim.Reps = 4
Sim.Seed = 42
Root.Seg = 0

[Indel]
Params.Ins = 1.039000, 50
Params.Ins = 1.039000, 100
Model.Ins = "GEO"
Rate.Ins = 0.01
Max.Ins = 50.0
Params.Del = 1.039000, 50
Rate.Ins = 0.1
Max.Ins = 100.0
Params.Del = 1.039000, 10
Model.Del = "POWER-LAW"
Rate.Del = 0.01
Max.Del = 50.0
Max.Del = 10.0

[[-]]
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.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"

Subst.Model = "f81"
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 = "CONST"
Root.Seg = 1

[[-]]
Tree.Tree = "(F:0.3, G:0.2)C;"
Subst.Model = "k2p"
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 = 3

Subst.Model = "tn"
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"

Subst.Model = "tn_f04"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(H:0.3, I:0.2)C;"
Subst.Model = "hky"
Subst.Rate.Model = "ZERO"
Root.Seg = 2

[[-]]
Tree.Tree = "(J:0.3, K:0.2)C;"
Subst.Model = "f84"
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 = 5

Subst.Model = "hky"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(L:0.3, M:0.2)C;"
Subst.Model = "f81"
Subst.Rate.Model = "ZERO"
Root.Seg = 6

Subst.Model = "jtt"
Subst.Freqs = 0.2, 0.3, 0.3, 0.2
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(N:0.3, O:0.2)C;"
Subst.Model = "tn"
Subst.Rate.Model = "ZERO"
Root.Seg = 7

Subst.Model = "dayhoff"
Subst.Freqs = 0.2, 0.3, 0.3, 0.22, 0.2222, 0.3112, 0.3333, 0.223, 0.2061, 0.3007, 0.3998, 0.2112, 0.244, 0.3726, 0.30871, 0.29191, 0.2232, 0.322, 0.32, 0.12
Subst.Params = 2.0, 1.0, 3.0, 1.0, 1.0, 1.0
[[-]]
Tree.Tree = "(P:0.3, Q:0.2)C;"
Subst.Model = "tn-f04"
Subst.Rate.Model = "ZERO"
Root.Seg = 8

0 comments on commit afff69b

Please sign in to comment.
You can’t perform that action at this time.