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<prev • 99 results • page 1 of 4 • next >
3
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dN/dS -1, in attempt to test purifying selection, CODEML PAML
paml codeml written 7 days ago by scheng25 • 10 • updated 7 days ago by lieven.sterck ♦ 5.2k
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2
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3.2k
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2
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CodeML Troubleshooting Help
evolution paml codeml written 4.4 years ago by p.juttyrajan • 0 • updated 8 weeks ago by biodianita • 0
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103
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0
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Theory question on dN/dS values for phylogeny
dnds codeml paml written 8 weeks ago by DNAngel • 30
1
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1
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179
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1
answer
How can I interpret the results of a likelihood ratio test between substitution models?
paml site models likelihood ratio test written 3 months ago by Mimmi Ahlmén • 10 • updated 8 weeks ago by Asaf ♦ 5.7k
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1
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177
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1
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Help with understanding PAML M0 output
paml m0 written 9 weeks ago by DNAngel • 30 • updated 8 weeks ago by Dave Carlson • 90
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2
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522
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2
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very high maximum-likelihood dS values from PAML
dn/ds alignment paml written 18 months ago by glarue • 20 • updated 11 weeks ago by Biostar ♦♦ 20
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2
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377
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5 follow
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Number of species for positive selection analysis
genome alignment evolution paml positive selection written 12 weeks ago by sammy.ich17 • 20 • updated 12 weeks ago by pltbiotech_tkarthi • 170
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1
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149
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1
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How do you run codeml for two genes in one file but with 1 species tree?
paml codeml written 3 months ago by DNAngel • 30 • updated 3 months ago by shelkmike • 130
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1
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299
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1
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PAML needs branch labels in tree
paml newick tree written 5 months ago by miles.thorburn • 80
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254
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Using and Understanding PAML for positive selection
gene phylogenetics paml ete selection written 3 months ago by lokdeep17 • 0
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209
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0
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Q. BioPython: CodeML FileNotFoundError: [WinError 2]
paml biopython written 4 months ago by mtbreeze • 0 • updated 4 months ago by Medhat ♦ 8.3k
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182
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0
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how to do a MK test analysis
mk test mcdonald-kreitman test paml written 4 months ago by Kay • 0
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234
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Problem with CODEML parameters
molecular evolution codeml paml written 4 months ago by aeonswhisper • 0
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275
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Issue with running Codeml using Biopython
paml python biopython codeml linux written 5 months ago by laurenmee17 • 0
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2
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1.1k
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2
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yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
pal2nal phylip paml input file written 23 months ago by shreyasibiswas88 • 30 • updated 6 months ago by al-ash • 100
0
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340
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0
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ete3 evol doesnt work on test data
ete3 paml ete written 7 months ago by Kay • 0 • updated 7 months ago by WouterDeCoster ♦ 39k
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2
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8.0k
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2
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Help With Understanding The Output Of Codeml From The Paml Package
paml codeml selection written 9.2 years ago by Joseph Hughes • 2.7k • updated 9 months ago by RamRS ♦ 22k
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228
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PAML NsSites sequence length influences significance?
nssites paml codeml written 9 months ago by susannak • 0
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417
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0
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Calculate dN/dS ratio for protein coding genes using PAML
rate anlysis paml rate analysis paml written 9 months ago by b.shrestha • 0
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654
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HyPhy or PAML: Testing Multiple Hypotheses with the same phylogeny/alignment?
hyphy phylogeny codon sequence paml written 17 months ago by space-slash-ellipsis • 0 • updated 9 months ago by Biostar ♦♦ 20
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413
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dN/dS within and between species
phylogeny hyphy mega paml msa written 12 months ago by krc3004 • 0
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1
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506
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1
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Error Running codeml
phylogeny alignment paml written 13 months ago by ammarsabir15 • 50 • updated 13 months ago by Sishuo Wang • 170
3
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1
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415
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1
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How to deal with one-to-many orthologies in PAML
dn/ds orthology paml written 14 months ago by Solowars • 50 • updated 14 months ago by lieven.sterck ♦ 5.2k
1
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1
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1.7k
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1
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Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
phylogeny substitution rates paml ds codeml written 2.6 years ago by BlastedBadger • 70 • updated 15 months ago by al-ash • 100
0
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542
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PAML: Codeml Foreground/background branch issue
paml written 16 months ago by j.a.yearsley • 10
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352
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CodeML 4.9e "strange: f[132] = -0.889877 very small" messages
phylogenetic paml codeml written 18 months ago by Hugo • 150
0
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1
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943
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1
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PAML CodeMl Dn/Ds help
paml codeml written 18 months ago by mti193 • 0
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1
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2.9k
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1
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Detailed instructions for how to use PAML
file format paml dn/ds ratio written 20 months ago by dixex • 0 • updated 20 months ago by h.mon ♦ 26k
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540
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PAMP Error: Error in sequence data file: L at 54 seq 1
paml written 20 months ago by dixex • 0
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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 20 months ago by ThulasiS • 60
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