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  • #1

    Site-wise Log-Likelihood

    Hello,

    I have several thousand sets of CDS from more 20 species. I would like to determine the Site-wise Log-Likelihood support for all amino acids for a given tree. Then I would like to compare the mean SSLS for each gene with an alternate tree. How do you obtain a list of SSLS values for a given set of CDSs for 20 species? If using PAML or RAxML, what commands will produce the correct file?

    Thanks,
    Ryan
    Tags: bioinfomatics, comparative genomics, evolutionary biology, paml, raxml
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