**280**wrote:

Hi,

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 !

**140**• written 8.1 years ago by Francois Olivier Hébert •

**280**

that's a really strange error! I'm sorry I have no clue to solve your problem. your explanation seems logically correct but that would mean that your sequences have 0 non-synonymous sites and how could it be possible?

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