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<prev • 103 results • page 1 of 4 • next >
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Interpretating PAML results from MSA of nuclear gene (RNAseq data)
paml rna-seq results written 13 days ago by zoe.postel • 0
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How to obtain protein-coding sequences from assembled genome/exome dataset?
paml bwa written 27 days ago by DNAngel • 40
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Codeml BEB positive sites don't match amino acids in alignment
positve selection branch-site model paml codeml written 6 weeks ago by maggie.bartlett • 0
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Ka/Ks (Or Dn/Ds) Calculation From Sequenced Transcriptome Contigs
paml written 6.8 years ago by tom.newport • 10 • updated 6 weeks ago by Adrian Pelin • 2.3k
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PAML codeML 4.8 wont give maximum likelihood nor omega estimates
dn/ds alignment paml written 3 months ago by mtd66 • 0
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dN/dS -1, in attempt to test purifying selection, CODEML PAML
paml codeml written 4 months ago by scheng25 • 10 • updated 3 months ago by Biostar ♦♦ 20
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CodeML Troubleshooting Help
evolution paml codeml written 4.7 years ago by p.juttyrajan • 0 • updated 6 months ago by biodianita • 0
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Theory question on dN/dS values for phylogeny
dnds codeml paml written 6 months ago by DNAngel • 40
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How can I interpret the results of a likelihood ratio test between substitution models?
paml site models likelihood ratio test written 7 months ago by Mimmi Ahlmén • 10 • updated 6 months ago by Asaf ♦ 6.4k
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Help with understanding PAML M0 output
paml m0 written 6 months ago by DNAngel • 40 • updated 6 months ago by Dave Carlson • 260
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very high maximum-likelihood dS values from PAML
dn/ds alignment paml written 23 months ago by glarue • 20 • updated 6 months ago by Biostar ♦♦ 20
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5 follow
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Number of species for positive selection analysis
genome alignment evolution paml positive selection written 7 months ago by sammy.ich17 • 20 • updated 7 months ago by pltbiotech_tkarthi • 170
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How do you run codeml for two genes in one file but with 1 species tree?
paml codeml written 7 months ago by DNAngel • 40 • updated 7 months ago by shelkmike • 130
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PAML needs branch labels in tree
paml newick tree written 9 months ago by miles.thorburn • 80
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Using and Understanding PAML for positive selection
gene phylogenetics paml ete selection written 8 months ago by lokdeep17 • 0
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Q. BioPython: CodeML FileNotFoundError: [WinError 2]
paml biopython written 8 months ago by mtbreeze • 0 • updated 8 months ago by Medhat ♦ 8.5k
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how to do a MK test analysis
mk test mcdonald-kreitman test paml written 8 months ago by Kay • 0
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Problem with CODEML parameters
molecular evolution codeml paml written 8 months ago by aeonswhisper • 0
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Issue with running Codeml using Biopython
paml python biopython codeml linux written 9 months ago by laurenmee17 • 0
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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 2.2 years ago by shreyasibiswas88 • 30 • updated 10 months ago by al-ash • 110
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ete3 evol doesnt work on test data
ete3 paml ete written 11 months ago by Kay • 0 • updated 11 months ago by WouterDeCoster ♦ 41k
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Help With Understanding The Output Of Codeml From The Paml Package
paml codeml selection written 9.5 years ago by Joseph Hughes • 2.7k • updated 13 months ago by RamRS ♦ 24k
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318
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PAML NsSites sequence length influences significance?
nssites paml codeml written 13 months ago by susannak • 0
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Calculate dN/dS ratio for protein coding genes using PAML
rate anlysis paml rate analysis paml written 13 months ago by b.shrestha • 0
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HyPhy or PAML: Testing Multiple Hypotheses with the same phylogeny/alignment?
hyphy phylogeny codon sequence paml written 22 months ago by space-slash-ellipsis • 0 • updated 13 months ago by Biostar ♦♦ 20
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dN/dS within and between species
phylogeny hyphy mega paml msa written 17 months ago by krc3004 • 10
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Error Running codeml
phylogeny alignment paml written 17 months ago by ammarsabir15 • 60 • updated 17 months ago by Sishuo Wang • 180
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How to deal with one-to-many orthologies in PAML
dn/ds orthology paml written 18 months ago by Solowars • 50 • updated 18 months ago by lieven.sterck ♦ 6.1k
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Get dS numbers _per branch_ with PAML codeml (or branch length estimates)
phylogeny substitution rates paml ds codeml written 3.0 years ago by BlastedBadger • 70 • updated 19 months ago by al-ash • 110
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PAML: Codeml Foreground/background branch issue
paml written 21 months ago by j.a.yearsley • 10
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