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<prev • 87 results • page 1 of 3 • next >
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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 16 months ago by shreyasibiswas88 • 30 • updated 4 days ago by al-ash • 60
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66
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ete3 evol doesnt work on test data
ete3 paml ete written 4 weeks ago by Kay • 0 • updated 4 weeks ago by WouterDeCoster ♦ 35k
4
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2
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7.6k
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2
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Help With Understanding The Output Of Codeml From The Paml Package
paml codeml selection written 8.6 years ago by Joseph Hughes • 2.6k • updated 3 months ago by RamRS ♦ 19k
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124
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PAML NsSites sequence length influences significance?
nssites paml codeml written 3 months ago by susannak • 0
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182
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Calculate dN/dS ratio for protein coding genes using PAML
rate anlysis paml rate analysis paml written 3 months ago by b.shrestha • 0
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461
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HyPhy or PAML: Testing Multiple Hypotheses with the same phylogeny/alignment?
hyphy phylogeny codon sequence paml written 11 months ago by space-slash-ellipsis • 0 • updated 3 months ago by Biostar ♦♦ 20
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2
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317
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2
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very high maximum-likelihood dS values from PAML
dn/ds alignment paml written 12 months ago by glarue • 20
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0
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237
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dN/dS within and between species
phylogeny hyphy mega paml msa written 6 months ago by krc3004 • 0
1
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1
answer
257
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1
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Error Running codeml
phylogeny alignment paml written 7 months ago by ammarsabir15 • 50 • updated 7 months ago by Sishuo Wang • 140
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1
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238
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1
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How to deal with one-to-many orthologies in PAML
dn/ds orthology paml written 7 months ago by Solowars • 40 • updated 7 months ago by lieven.sterck • 3.3k
1
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1
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1.3k
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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 2.1 years ago by BlastedBadger • 50 • updated 8 months ago by al-ash • 60
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344
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0
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PAML: Codeml Foreground/background branch issue
paml written 10 months ago by j.a.yearsley • 10
1
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0
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252
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0
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CodeML 4.9e "strange: f[132] = -0.889877 very small" messages
phylogenetic paml codeml written 12 months ago by Hugo • 140
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1
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660
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1
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PAML CodeMl Dn/Ds help
paml codeml written 12 months ago by mti193 • 0
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1
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1.7k
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1
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Detailed instructions for how to use PAML
file format paml dn/ds ratio written 13 months ago by dixex • 0 • updated 13 months ago by h.mon ♦ 21k
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0
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373
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0
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PAMP Error: Error in sequence data file: L at 54 seq 1
paml written 13 months ago by dixex • 0
0
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0
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364
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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 14 months ago by ThulasiS • 60
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538
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Should I average dN/dS over all CDS for a gene or consider only the longest transcript?
longest transcript average dn/ds dnds paml written 14 months ago by shreyasibiswas88 • 30
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0
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480
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codeml, output tree topology different from the input tree
paml codeml written 15 months ago by stolarek.ir • 550
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1
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504
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1
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How much does cleandata in PAML analysis remove?
paml codeml cleandata written 16 months ago by DNAngel • 20 • updated 16 months ago by h.mon ♦ 21k
1
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1
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1.7k
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1
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Should I Fix Branch Length In Paml Analyses?
evolution paml selection written 5.2 years ago by qiyunzhu • 420 • updated 16 months ago by Lhl • 730
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0
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553
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PAML sample sizes within multiple alignment format
software phylogenetic paml baseml likelihood written 21 months ago by enrightnm • 0
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1
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957
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1
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what is pairwise dN/dS used for?
gene dn/ds sequence paml written 21 months ago by dukecomeback • 40 • updated 21 months ago by Alex Reynolds ♦ 26k
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0
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595
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0
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PAML and WAG+gamma model
gamma paml codeml written 23 months ago by martanit • 0 • updated 23 months ago by Biostar ♦♦ 20
1
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1
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2.0k
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1
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Positive Selection And Evolutionary Model Selection
paml written 4.8 years ago by Pappu • 1.8k • updated 2.3 years ago by Brice Sarver • 2.5k
9
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3
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7.4k
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8 follow
3
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How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
paml written 5.8 years ago by Nari • 860 • updated 2.3 years ago by wangqingqing • 0
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1
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887
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1
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Codeml error - format problem?
dn/ds paml codeml written 2.3 years ago by natasha • 100 • updated 2.3 years ago by rstuder • 0
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0
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962
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0
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Ks calculation discrepancy (yn00 PAML, MEGA6 nei gojobori)
ks yn00 paml mega6 nei gojobori written 2.4 years ago by jomaco • 190
2
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1
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843
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1
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Calculating LRT of a phylogenetic tree (as in codeml)
paml codeml lrt written 2.4 years ago by spiral01 • 70 • updated 2.4 years ago by Brice Sarver • 2.5k
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1
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How to calculate dN/dS values?
genome dn/ds paml pal2nal written 2.4 years ago by utkarsh.sood • 30 • updated 2.4 years ago by Sej Modha ♦ 3.9k
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