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
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