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<prev • 112 results • page 1 of 4 • next >
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"Seq #20 occurs more than once in the tree" error from pam codeml analysis
phylogenetics paml codeml selection written 21 days ago by kathyd1994 • 0 • updated 20 days ago by Diana MoSa • 10
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Trying to use PAML to reconstruct ancestral sequences, but the output file is blank
paml written 9 weeks ago by tuj92050 • 0
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How to interpret codeml ?
hyphy meme paml codeml selection written 3 months ago by sahoo.sshree • 0
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Some problems about CODEML
positive selection sites paml codeml written 5.0 years ago by Ginsea Chen • 130 • updated 3 months ago by Biostar ♦♦ 20
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Mutation Selection test FMutSel0-M0 (Null) FMutSel-M0 (Alternative) df=0, how to do Chi square test?
paml codeml written 7 months ago by kabir.deb0353 • 10 • updated 5 months ago by Biostar ♦♦ 20
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Codon substitution model (codeml)
dnds codeml paml written 7 months ago by Chvatil • 40 • updated 5 months ago by Biostar ♦♦ 20
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12 follow
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How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
paml written 7.4 years ago by Nari • 880 • updated 7 months ago by Vincent Ranwez • 30
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Gene size and power of detection in evolutionary rates analysis
gene molecular clock paml codeml evolutionary rate written 7 months ago by pr • 10
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How to calculate rate of synonymous substitution at 4 fold and 2 fold degenerate sites?
gene substitution paml written 7 months ago by kabir.deb0353 • 10 • updated 7 months ago by Pierre Lindenbaum ♦ 129k
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Syntax highlighting for PAML's control files in Vim
vim paml written 8 months ago by BlastedBadger • 90
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How can I understand Codeml assigned Internal Branch Numbers To Phylogenetic Trees from mlc file?
paml codeml written 8 months ago by kabir.deb0353 • 10
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PAMP Error: Error in sequence data file: L at 54 seq 1
paml written 2.8 years ago by dixex • 0 • updated 9 months ago by zx8754 ♦ 9.4k
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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 3.0 years ago by shreyasibiswas88 • 30 • updated 9 months ago by xiaotong.wang • 0
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Interpretating PAML results from MSA of nuclear gene (RNAseq data)
paml rna-seq results written 9 months ago by zoe.postel • 0
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How to obtain protein-coding sequences from assembled genome/exome dataset?
paml bwa written 10 months ago by DNAngel • 60
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183
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Codeml BEB positive sites don't match amino acids in alignment
positve selection branch-site model paml codeml written 10 months ago by maggie.bartlett • 0
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Ka/Ks (Or Dn/Ds) Calculation From Sequenced Transcriptome Contigs
paml written 7.6 years ago by tom.newport • 10 • updated 11 months ago by Adrian Pelin • 2.4k
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PAML codeML 4.8 wont give maximum likelihood nor omega estimates
dn/ds alignment paml written 12 months ago by mtd66 • 0
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dN/dS -1, in attempt to test purifying selection, CODEML PAML
paml codeml written 13 months ago by scheng25 • 10 • updated 12 months ago by Biostar ♦♦ 20
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2
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CodeML Troubleshooting Help
evolution paml codeml written 5.5 years ago by p.juttyrajan • 0 • updated 15 months ago by Diana MoSa • 10
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Theory question on dN/dS values for phylogeny
dnds codeml paml written 15 months ago by DNAngel • 60
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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 17 months ago by Mimmi Ahlmén • 20 • updated 15 months ago by Asaf ♦ 8.3k
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683
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Help with understanding PAML M0 output
paml m0 written 15 months ago by DNAngel • 60 • updated 15 months ago by Dave Carlson • 320
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very high maximum-likelihood dS values from PAML
dn/ds alignment paml written 2.7 years ago by glarue • 40 • updated 16 months ago by Biostar ♦♦ 20
4
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803
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5 follow
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Number of species for positive selection analysis
genome alignment evolution paml positive selection written 16 months ago by sammy.ich17 • 20 • updated 16 months ago by pltbiotech_tkarthi • 180
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446
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How do you run codeml for two genes in one file but with 1 species tree?
paml codeml written 17 months ago by DNAngel • 60 • updated 17 months ago by shelkmike • 230
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1
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920
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PAML needs branch labels in tree
paml newick tree written 19 months ago by miles.thorburn • 100
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Using and Understanding PAML for positive selection
gene phylogenetics paml ete selection written 17 months ago by lokdeep17 • 0
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Q. BioPython: CodeML FileNotFoundError: [WinError 2]
paml biopython written 18 months ago by mtbreeze • 0 • updated 18 months ago by Medhat ♦ 8.7k
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505
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how to do a MK test analysis
mk test mcdonald-kreitman test paml written 18 months ago by Kay • 0
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