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• How can I calculate p value for rate analysis of particular lineage?
  How can I calculate p value for rate analysis of particular lineage? I have used Mega 6 for estim...
• dN/dS analysis of genomes
  Dear All, I have done several analysis to find dN/dS ratio in six species. 1. I found one-to-on...
• How to go from proteome of species A and compare genes to species B
  I have a transcriptome of a parasite (B) and want to do a dN/dS analysis. I have downloaded the F...
• Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
  Biopython comes with methods to interface with the PAML package for phylogenetic analysis. In pa...
• Codeml- Dn/Ds High Due To The Low Ds
  Hi All, I am new to codeml analysis. I have done the codeml analysis on a set of genes using bot...
• Can the Matlab dn/ds function take more than two sequences?
  Hi all, I have a relatively simple question. I'm trying to perform a dn/ds analysis on a set of ...
• Calculate dN/dS ratio for protein coding genes using PAML
  Hi, I am trying to calculate dN/dS ratio for protein coding genes. I have sequence alignment for...
• Does PAML (codeml ) analysis include the introns or it correspond only to the CDS ?
  I have done a phylogeny tree using protein sequences. Now i want to measure dn/ds on several bran...
• How to calculate dN/dS values?
  Hello, I have made a codon alignment using pal2nal and generated a .codon file. Now I want to ca...
• Should I average dN/dS over all CDS for a gene or consider only the longest transcript?
  Hi everyone, I have calculated dN/dS ratio for ALL transcripts for ALL genes for my study system...
• Dn/ds for human orthologus?
  1.how to calculate dn/ds ratio for list of mrna and lncrna from mouse data against human ? 2.I h...
• dN/dS within and between species
  Hi all, Recently I have been very interested in calculating the dN/dS ratio to estimate rates of...
• Recommendations for dN/dS software for balancing selection scan
  I am looking to systematically scan genomes for balancing selection. However, I am going to be do...
• Calculate Average Dn And Ds For Gene Families
  hi, all I have several single-copy gene families identified from 12 genomes, Now I want to know ...
• Orthologous Genes And Dn/Ds Ratio
  Hi everyone, I have a list of orthologous genes and a species tree, I would like to know how to ...
• How Can I Use Paml To Calculate The Dn/Ds Value Of Only Some Specific Branches?
  Since it often takes a long time to calculate the dN/dS value of a big tree, how can I calculate ...
• 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. Shal...