Dear Azhar sahb,

The PAML package here are different tools inside. out of them the yn00 software, that compute dN/dS in a pair-wise manner between two sequences:

http://abacus.gene.ucl.ac.uk/software/paml.html

Hi,

the yn00 code was packed and cinveniently separated for analyzing either unaligned or pre-aligned sequences at https://github.com/hyphaltip/subopt-kaks ,

hope this helps,

Bruno

Thanks all,

Dear Aqeal sahib

                  my question is can I use biomart orthlogu option which also gives dn/ds ratio for each ortholgu then I can just take sum of dn/ds to see result ?

Hi! you may indeed take the average of dN/dS ratio for all orthologous pair separately from mRNA and lncRNA and then draw your conclusion like this one,

https://www.biostars.org/p/5817/