Synonymous sites only for tree inference

[ksw]

Hi all,

I'm wondering if there is a PAML option to identify synonymous sites in a DNA multiple sequence alignment and infer phylogenies with this subset of sites alone? 

I am working with a multiple sequence alignment (DNA) of ~70 virus samples with limited genetic diversity. My goal is to subset the multiple sequence alignment including synonymous sites only, because we believe that there are parallel non-synonymous mutations occurring that do not provide information on shared evolutionary history.

Thank you in advance and best,

[Ziheng]

perhaps you can use the 3rd codon positions.

alternatively you can use the so called 4-fold degenerate sites.

apparently if you use verbose = 2, codeml prints out an alignment of 4-fold degenerate sites only in a file with the name like 4fold.

ziheng