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<prev • 69 results • page 1 of 3 • next >
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Codeml BEB positive sites don't match amino acids in alignment
positve selection branch-site model paml codeml written 4 days ago by maggie.bartlett • 0
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dN/dS -1, in attempt to test purifying selection, CODEML PAML
paml codeml written 3 months ago by scheng25 • 10 • updated 8 weeks ago by Biostar ♦♦ 20
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Error: err: option file. add space around the equal sign?.
software error codeml written 3 months ago by dudka • 0 • updated 3 months ago by RamRS ♦ 24k
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CodeML Troubleshooting Help
evolution paml codeml written 4.6 years ago by p.juttyrajan • 0 • updated 4 months ago by biodianita • 0
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Theory question on dN/dS values for phylogeny
dnds codeml paml written 4 months ago by DNAngel • 30
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337
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How to identify Substitution rate is per time unit in baseml
baseml substitution rate codeml written 6 months ago by aloke205 • 30
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Need help regarding hypothesis of branch model
branch-site models codeml written 5 months ago by rprog008 • 30
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Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
phylogenetic tree codeml positive selection written 5 months ago by rprog008 • 30
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How do you run codeml for two genes in one file but with 1 species tree?
paml codeml written 6 months ago by DNAngel • 30 • updated 6 months ago by shelkmike • 130
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Problem with CODEML parameters
molecular evolution codeml paml written 7 months ago by aeonswhisper • 0
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Issue with running Codeml using Biopython
paml python biopython codeml linux written 8 months ago by laurenmee17 • 0
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Help With Understanding The Output Of Codeml From The Paml Package
paml codeml selection written 9.4 years ago by Joseph Hughes • 2.7k • updated 12 months ago by RamRS ♦ 24k
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PAML NsSites sequence length influences significance?
nssites paml codeml written 12 months ago by susannak • 0
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calculating dn/ds from codeml output
codeml written 15 months ago by RT • 340
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Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
phylogeny substitution rates paml ds codeml written 2.9 years ago by BlastedBadger • 70 • updated 18 months ago by al-ash • 110
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CodeML 4.9e "strange: f[132] = -0.889877 very small" messages
phylogenetic paml codeml written 21 months ago by Hugo • 150
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PAML CodeMl Dn/Ds help
paml codeml written 21 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 23 months ago by ThulasiS • 60
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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 23 months ago by ThulasiS • 60
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codeml, output tree topology different from the input tree
paml codeml written 2.0 years ago by stolarek.ir • 600
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How much does cleandata in PAML analysis remove?
paml codeml cleandata written 2.1 years ago by DNAngel • 30 • updated 2.1 years ago by h.mon ♦ 27k
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use codeml to investigate positive selection in xenologs
codeml xenolog written 2.5 years ago by Elahe Rabiei-Motlagh • 10
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PAML and WAG+gamma model
gamma paml codeml written 2.7 years ago by martanit • 0 • updated 2.7 years ago by Biostar ♦♦ 20
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1.1k
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1
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Codeml error - format problem?
dn/ds paml codeml written 3.1 years ago by natasha • 100 • updated 3.1 years ago by rstuder • 0
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Calculating LRT of a phylogenetic tree (as in codeml)
paml codeml lrt written 3.1 years ago by spiral01 • 100 • updated 3.1 years ago by Brice Sarver • 2.9k
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How to calculate p-value from codeml likelihood ratio test results for Benjamini-Hochberg correction
statistics paml codeml lrt written 3.5 years ago by memory_donk • 250
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Biopython PAML CodeML Error [Errno 2]
biopython codeml paml written 3.5 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 3.7 years ago by Dave Carlson • 120
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How to interpret LRT < 0 in codeml branch-model based test?
codeml branch-model likelihood ratio test written 3.8 years ago by sckinta • 550 • updated 3.8 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 3.8 years ago by sckinta • 550
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