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Old 12-27-2013, 09:35 AM   #1
rdoan
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Location: USA

Join Date: Oct 2012
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Default 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
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bioinfomatics, comparative genomics, evolutionary biology, paml, raxml

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