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<prev • 120 results • page 1 of 4 • next >
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Question about codeml
phylogeny tree paml ds codeml written 5 weeks ago by Chvatil • 50
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100
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Phylogenetic requirements for generating dN/dS
dn/ds paml codeml written 7 weeks ago by benjamin.aaron.taylor • 0
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166
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Runmode = -2 in Biopython PAML impossible ?
python3 paml codeml biopython written 7 weeks ago by Chvatil • 50
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108
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Programme to calculate dN/dS between pair of sequences in a seq alignment
gene dn/ds sequence paml codeml written 8 weeks ago by Chvatil • 50
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93
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SWAMP (Sliding Window Alignment Masker for PAML) | Error with Branch Code File
ugene swamp alignment jalview paml written 10 weeks ago by Continuum.DLH • 0
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108
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PAML sample size question and variation in results
paml written 11 weeks ago by DNAngel • 90
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163
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Understanding PAML results between random-sites and clade model C.
paml written 3 months ago by DNAngel • 90
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161
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CODEML: Ideal setting for generating dn/ds values for a gene family within a species.
paml codeml written 3 months ago by venura • 60
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1
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167
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1
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"Seq #20 occurs more than once in the tree" error from pam codeml analysis
phylogenetics paml codeml selection written 6 months ago by kathyd1994 • 0 • updated 6 months ago by Diana MoSa • 20
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200
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Trying to use PAML to reconstruct ancestral sequences, but the output file is blank
paml written 7 months ago by tuj92050 • 0
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185
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How to interpret codeml ?
hyphy meme paml codeml selection written 9 months ago by sahoo.sshree • 0
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1.7k
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Some problems about CODEML
positive selection sites paml codeml written 5.4 years ago by Ginsea Chen • 130 • updated 9 months ago by Biostar ♦♦ 20
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209
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Mutation Selection test FMutSel0-M0 (Null) FMutSel-M0 (Alternative) df=0, how to do Chi square test?
paml codeml written 13 months ago by kabir.deb0353 • 10 • updated 11 months ago by Biostar ♦♦ 20
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229
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Codon substitution model (codeml)
dnds codeml paml written 13 months ago by Chvatil • 50 • updated 11 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 7.9 years ago by Nari • 880 • updated 13 months ago by Vincent Ranwez • 30
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180
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Gene size and power of detection in evolutionary rates analysis
gene molecular clock paml codeml evolutionary rate written 13 months ago by pr • 10
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327
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How to calculate rate of synonymous substitution at 4 fold and 2 fold degenerate sites?
gene substitution paml written 13 months ago by kabir.deb0353 • 10 • updated 13 months ago by Pierre Lindenbaum ♦ 133k
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200
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1
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Syntax highlighting for PAML's control files in Vim
vim paml written 13 months ago by BlastedBadger • 90
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174
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How can I understand Codeml assigned Internal Branch Numbers To Phylogenetic Trees from mlc file?
paml codeml written 13 months ago by kabir.deb0353 • 10
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885
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PAMP Error: Error in sequence data file: L at 54 seq 1
paml written 3.2 years ago by dixex • 0 • updated 14 months ago by zx8754 ♦ 9.9k
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3
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2.2k
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3
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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 3.5 years ago by shreyasibiswas88 • 30 • updated 14 months ago by xiaotong.wang • 0
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303
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Interpretating PAML results from MSA of nuclear gene (RNAseq data)
paml rna-seq results written 15 months ago by zoe.postel • 0
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321
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How to obtain protein-coding sequences from assembled genome/exome dataset?
paml bwa written 15 months ago by DNAngel • 90
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266
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Codeml BEB positive sites don't match amino acids in alignment
positve selection branch-site model paml codeml written 16 months ago by maggie.bartlett • 0
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2
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4.3k
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2
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Ka/Ks (Or Dn/Ds) Calculation From Sequenced Transcriptome Contigs
paml written 8.1 years ago by tom.newport • 10 • updated 16 months ago by Adrian Pelin • 2.4k
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570
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PAML codeML 4.8 wont give maximum likelihood nor omega estimates
dn/ds alignment paml written 18 months ago by mtd66 • 0
3
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652
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dN/dS -1, in attempt to test purifying selection, CODEML PAML
paml codeml written 19 months ago by scheng25 • 10 • updated 18 months ago by Biostar ♦♦ 20
2
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2
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4.9k
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2
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CodeML Troubleshooting Help
evolution paml codeml written 6.0 years ago by p.juttyrajan • 0 • updated 21 months ago by Diana MoSa • 20
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401
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Theory question on dN/dS values for phylogeny
dnds codeml paml written 21 months ago by DNAngel • 90
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983
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1
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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 22 months ago by Mimmi Ahlmén • 20 • updated 21 months ago by Asaf ♦ 8.5k
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