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<prev • 86 results • page 1 of 3 • next >
4
votes
2
answers
7.5k
views
2
answers
Help With Understanding The Output Of Codeml From The Paml Package
paml codeml selection written 8.4 years ago by Joseph Hughes • 2.6k • updated 11 days ago by Ram ♦ 17k
0
votes
0
answers
68
views
0
answers
PAML NsSites sequence length influences significance?
nssites paml codeml written 12 days ago by susannak • 0
0
votes
0
answers
80
views
0
answers
Calculate dN/dS ratio for protein coding genes using PAML
rate anlysis paml rate analysis paml written 13 days ago by b.shrestha • 0
1
vote
0
answers
370
views
0
answers
HyPhy or PAML: Testing Multiple Hypotheses with the same phylogeny/alignment?
hyphy phylogeny codon sequence paml written 8 months ago by space-slash-ellipsis • 0 • updated 14 days ago by Biostar ♦♦ 20
0
votes
2
answers
261
views
2
answers
very high maximum-likelihood dS values from PAML
dn/ds alignment paml written 9 months ago by glarue • 0
0
votes
1
answer
612
views
1
answer
yn00 in PAML returns error: Error in sequence data file: E at 3 seq 1.
pal2nal phylip paml input file written 13 months ago by shreyasibiswas88 • 30 • updated 3 months ago by lxw34 • 0
0
votes
0
answers
171
views
0
answers
dN/dS within and between species
phylogeny hyphy mega paml msa written 3 months ago by krc3004 • 0
1
vote
1
answer
175
views
1
answer
Error Running codeml
phylogeny alignment paml written 4 months ago by ammarsabir15 • 50 • updated 4 months ago by Sishuo Wang • 140
2
votes
1
answer
170
views
1
answer
How to deal with one-to-many orthologies in PAML
dn/ds orthology paml written 5 months ago by Solowars • 30 • updated 5 months ago by lieven.sterck • 2.2k
1
vote
1
answer
1.2k
views
1
answer
Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
phylogeny substitution rates paml ds codeml written 22 months ago by BlastedBadger • 50 • updated 5 months ago by al-ash • 50
0
votes
0
answers
273
views
0
answers
PAML: Codeml Foreground/background branch issue
paml written 7 months ago by j.a.yearsley • 10
1
vote
0
answers
219
views
0
answers
CodeML 4.9e "strange: f[132] = -0.889877 very small" messages
phylogenetic paml codeml written 9 months ago by Hugo • 130
0
votes
1
answer
540
views
1
answer
PAML CodeMl Dn/Ds help
paml codeml written 9 months ago by mti193 • 0
0
votes
1
answer
1.2k
views
1
answer
Detailed instructions for how to use PAML
file format paml dn/ds ratio written 10 months ago by dixex • 0 • updated 10 months ago by h.mon ♦ 19k
0
votes
0
answers
317
views
0
answers
PAMP Error: Error in sequence data file: L at 54 seq 1
paml written 10 months ago by dixex • 0
0
votes
0
answers
321
views
0
answers
What would be the best model to calcualte dn/ds ratio of genes of bacterial strains?
dn/ds paml codeml kaks written 11 months ago by ThulasiS • 60
0
votes
0
answers
437
views
0
answers
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 11 months ago by shreyasibiswas88 • 30
0
votes
0
answers
417
views
0
answers
codeml, output tree topology different from the input tree
paml codeml written 12 months ago by stolarek.ir • 550
0
votes
1
answer
438
views
1
answer
How much does cleandata in PAML analysis remove?
paml codeml cleandata written 13 months ago by balasink • 10 • updated 13 months ago by h.mon ♦ 19k
1
vote
1
answer
1.7k
views
1
answer
Should I Fix Branch Length In Paml Analyses?
evolution paml selection written 5.0 years ago by qiyunzhu • 420 • updated 13 months ago by Lhl • 730
0
votes
0
answers
491
views
0
answers
PAML sample sizes within multiple alignment format
software phylogenetic paml baseml likelihood written 18 months ago by enrightnm • 0
0
votes
1
answer
834
views
1
answer
what is pairwise dN/dS used for?
gene dn/ds sequence paml written 18 months ago by dukecomeback • 40 • updated 18 months ago by Alex Reynolds ♦ 25k
0
votes
0
answers
544
views
0
answers
PAML and WAG+gamma model
gamma paml codeml written 21 months ago by martanit • 0 • updated 20 months ago by Biostar ♦♦ 20
1
vote
1
answer
1.9k
views
1
answer
Positive Selection And Evolutionary Model Selection
paml written 4.5 years ago by Pappu • 1.8k • updated 2.0 years ago by Brice Sarver • 2.5k
9
votes
3
answers
7.1k
views
8 follow
3
answers
How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
paml written 5.5 years ago by Nari • 860 • updated 2.0 years ago by wangqingqing • 0
0
votes
1
answer
819
views
1
answer
Codeml error - format problem?
dn/ds paml codeml written 2.1 years ago by natasha • 100 • updated 2.1 years ago by rstuder • 0
0
votes
0
answers
868
views
0
answers
Ks calculation discrepancy (yn00 PAML, MEGA6 nei gojobori)
ks yn00 paml mega6 nei gojobori written 2.1 years ago by jomaco • 180
2
votes
1
answer
745
views
1
answer
Calculating LRT of a phylogenetic tree (as in codeml)
paml codeml lrt written 2.1 years ago by spiral01 • 70 • updated 2.1 years ago by Brice Sarver • 2.5k
0
votes
1
answer
1.8k
views
1
answer
How to calculate dN/dS values?
genome dn/ds paml pal2nal written 2.1 years ago by utkarsh.sood • 30 • updated 2.1 years ago by Sej Modha ♦ 3.6k
2
votes
0
answers
1.0k
views
0
answers
dN/dS in a tree (multiple genes)
kaks dn/ds phylogenetics paml dnds written 2.3 years ago by BlastedBadger • 50
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