I have a set of 383 coding sequences in which there is a whole bunch of SNPs. I only have two species (2 populations representing incipient species). I used PAML to estimate the dn/ds ratio for each sequence. For some of the sequences, I get negative values either for dn, ds or dn/ds.
I know from the FAQs PDF file that comes with PAML's latest distribution that -1.000 means infinity. So if you have a dn > 0 and a ds = 0, when you divide dn by ds, you get -1.0000, i.e infinity. But when I get a result such as :
Nei & Gojobori 1986. dN/dS (dN, dS) (Note: This matrix is not used in later ML. analysis. Use runmode = -2 for ML pairwise comparison.) allele1 allele2 -0.6057 (-1.0000 1.6509)
How is it possible to have an infinite value for dn OR ds ? dn = -1.0000 or ds = -1.0000 seems really strange to me. How should I interpret these negative values ? My guess would be that it means that there is no synonymous or non-synonymous sites in the sequence. Thus, PAML divides 0 by 0 and it returns -1.0000. Example: if there is 0 synonymous mutations and 0 synonymous sites, the ratio of synonymous mutation / synonymous sites equals infinity (-1.0000) because it's a division by 0.
Am I wrong ? If not, should I simply replace the value -1.0000 by 0 each time dn or ds equals -1.0000 ?
Thank you for any help !