User: rprog008

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rprog00830
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Posts by rprog008

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Comment: C: Number of species for positive selection analysis
... read again my first comment... 😑☺ i said less than 10 may be questionable sometime.. i never said always. others too are claiming going for 10 sequence is a rule of thumb. one of the reason already stated by aloke and others. my intention was to state why not to play safe rather than repeating you ...
written 12 weeks ago by rprog00830
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Comment: C: Number of species for positive selection analysis
... Thanks @aloke205 for this reference. I remember now, where i have read this. :) To @pltbiotech_tkarthi, if you read my first answer below careful ( for your kind reference), i have written " With less than 10 sequences, result obtained from PAML are sometime questionable?" now you know why it is qu ...
written 12 weeks ago by rprog00830
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Comment: C: Number of species for positive selection analysis
... Leave it !!! You are not understanding your own question. You just need to prove that others are wrong then you have to prove it. Sometime we need to use our brain too. Have you ever thought if we are taking single copy ortholog of each species, what does that means? Here each sequence represent a ...
written 12 weeks ago by rprog00830
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Comment: C: Number of species for positive selection analysis
... Read this discussion on researchgate, where one member have written - 4 species is on the smaller scale. If you do not have >10 sequences, you just don't have much power for detecting specific sites under positive selection (Murrell et al, 2010 - considering site classes are considered fixed eff ...
written 12 weeks ago by rprog00830
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Comment: C: Number of species for positive selection analysis
... As i said in the beginning of my answer, I can't remember where I have read this.. so at present there is no reference :) We strictly follow this rule because most the time reviewer asked analysis of large data set. if you are lucky, reviewer will not comment on smaller dataset but if unlucky, revie ...
written 12 weeks ago by rprog00830
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Answer: A: Number of species for positive selection analysis
... Kind notice: At present I can't remember where I have read this but would like to share with you the information below Generally, number of species should not be less than 10. With less than 10 sequences, result obtained from PAML are sometime questionable. So we should always perform PAML with at ...
written 12 weeks ago by rprog00830
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Need help regarding hypothesis of branch model
... ![enter image description here][1]Respected member, I am new learner of codeml and designing my experiment for analysis of 14 mammalian coding sequence based on the tutorial at https://link.springer.com/protocol/10.1007%2F978-1-4939-1438-8_4. In my analysis, human is “foreground branch”. I am ge ...
branch-site models codeml written 12 weeks ago by rprog00830
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Comment: A: Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
... Thanks. I will generate phylogenetic tree for each gene then :) ...
written 12 weeks ago by rprog00830
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Can i use consensus phylogenetic tree for calculation of dn/ds via codeml?
... I am trying to calculate dn/ds of about 3000 genes amongst 14 mammalian species via codeml. Shall i use already established phylogeny tree of these 14 mammalian species or shall i generate phylogenetic tree of each genes separately before codeml analysis Please help ...
phylogenetic tree codeml positive selection written 12 weeks ago by rprog00830
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(Closed) Can we call mechanistic codon model as parametric codon model ?
... Can I write mechanistic codon model as parametric codon model in my manuscript ? ...
substitution matric evolution written 3 months ago by rprog00830

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