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<prev • 63 results • page 1 of 3 • next >
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How to identify Substitution rate is per time unit in baseml
baseml substitution rate codeml written 9 days ago by aloke205 • 10
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88
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How do you run codeml for two genes in one file but with 1 species tree?
paml codeml written 25 days ago by DNAngel • 20 • updated 24 days ago by shelkmike • 130
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CodeML Troubleshooting Help
evolution paml codeml written 4.1 years ago by p.juttyrajan • 0 • updated 29 days ago by k.balaji93 • 10
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157
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Problem with CODEML parameters
molecular evolution codeml paml written 7 weeks ago by aeonswhisper • 0
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160
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Issue with running Codeml using Biopython
paml python biopython codeml linux written 10 weeks ago by laurenmee17 • 0
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Help With Understanding The Output Of Codeml From The Paml Package
paml codeml selection written 8.9 years ago by Joseph Hughes • 2.7k • updated 6 months ago by RamRS ♦ 20k
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PAML NsSites sequence length influences significance?
nssites paml codeml written 6 months ago by susannak • 0
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264
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calculating dn/ds from codeml output
codeml written 9 months ago by RT • 330
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Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
phylogeny substitution rates paml ds codeml written 2.4 years ago by BlastedBadger • 70 • updated 12 months ago by al-ash • 100
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CodeML 4.9e "strange: f[132] = -0.889877 very small" messages
phylogenetic paml codeml written 15 months ago by Hugo • 150
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PAML CodeMl Dn/Ds help
paml codeml written 16 months ago by mti193 • 0
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How to analyze multiple codeml output files to find out positive gene clusters?
perl python codeml written 17 months ago by ThulasiS • 60
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419
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What would be the best model to calcualte dn/ds ratio of genes of bacterial strains?
dn/ds paml codeml kaks written 18 months ago by ThulasiS • 60
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codeml, output tree topology different from the input tree
paml codeml written 18 months ago by stolarek.ir • 580
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How much does cleandata in PAML analysis remove?
paml codeml cleandata written 19 months ago by DNAngel • 20 • updated 19 months ago by h.mon ♦ 24k
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use codeml to investigate positive selection in xenologs
codeml xenolog written 24 months ago by Elahe Rabiei-Motlagh • 10
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PAML and WAG+gamma model
gamma paml codeml written 2.2 years ago by martanit • 0 • updated 2.2 years ago by Biostar ♦♦ 20
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970
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Codeml error - format problem?
dn/ds paml codeml written 2.6 years ago by natasha • 100 • updated 2.6 years ago by rstuder • 0
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1
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1
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Calculating LRT of a phylogenetic tree (as in codeml)
paml codeml lrt written 2.6 years ago by spiral01 • 80 • updated 2.6 years ago by Brice Sarver • 2.5k
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1
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How to calculate p-value from codeml likelihood ratio test results for Benjamini-Hochberg correction
statistics paml codeml lrt written 3.0 years ago by memory_donk • 230
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Biopython PAML CodeML Error [Errno 2]
biopython codeml paml written 3.0 years ago by QVH • 10
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codeml jobs taking much longer on a server than on an imac
latest sequence codeml written 3.2 years ago by Dave Carlson • 40
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1
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How to interpret LRT < 0 in codeml branch-model based test?
codeml branch-model likelihood ratio test written 3.3 years ago by sckinta • 480 • updated 3.3 years ago by abascalfederico • 1.1k
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How to specify a branch in the tree automatically for branch-site model codeml?
tree codeml written 3.4 years ago by sckinta • 480
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Some problems about CODEML
positive selection sites paml codeml written 3.6 years ago by Ginsea Chen • 120 • updated 3.4 years ago by Biostar ♦♦ 20
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Datamonkey vs. Codeml - differences in results
datamonkey paml codeml written 3.6 years ago by nichlieh • 0
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1
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Error running certain PAML - CodeML sequences
ka/ks sequence alignment paml codeml written 3.8 years ago by gyler75 • 0 • updated 3.8 years ago by Brice Sarver • 2.5k
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Constructing the ancestral state of amino acid
paml codeml selection written 3.9 years ago by RT • 330 • updated 3.8 years ago by Michael Dondrup ♦ 45k
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The best way to use PAML to analyze genes found only in some species on my tree
dn/ds alignment paml codeml written 3.9 years ago by seb85il • 0
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Practical questions with PAML(codeml)
paml codeml written 3.9 years ago by makebala • 0
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