Nucleotide to amino acid translation + synonymous/non-synonymous count

[Darth Ghisus]

Hi everybody,

I'm going to perform a SNP calling using SAMtools.
The source data consist of an invertebrate mitochondrial transcriptome and I would like to detect the synonymous and non-synonymous SNPs in order to perform some evolutionary tests, like Ka/Ks.
Basically, all I need is the number of synonymous and non-synonymous SNPs.

If no program is available, I could translate all the sequences and count those who match the reference amino acid sequence and those who don't. But I need a program to translate all my sequences from nucleotides to amino acid (using invertebrate mitochondrial code).
Suggestions?

Thanks a lot.

Fabrizio

P.S.: Softwares like Annovar are not useful to me, because I don't need a functional evaluation of my SNPs and, besides, I'm working on a non-model organism, so that kind of information is unavailable.

Cheers!!

[TiborNagy]

I think SIFT is your program.

[Balat]

you could also try 'popoolation'.