SNP frequencies in Fasta Alignment

Question

[Eva_Maria]

Hai everyone

I have a set of fasta aligned file from this alignment file how i will get snps and its frequencies

[Fabio Marroni]

Hi! In general, the more detail you provide, the higher is the chance that someone can help you. For example:

1) What do you mean by "fasta aligned files"?

2) How did you align them and what do they represent?

3) Do you have one fasta file for each individual you sequenced?

[Eva_Maria]

i aligned 20 genes (fasta format) using MAFFT and i want to find gene variation respect to snp/snp frequencies

Answer 1

[Fabio Marroni]

For any position do this:

1) Count all the different nucleotides (I assume for simplicity there are only two kinds, A and G).

2) Count how many As, count how many Gs.

3) The frequency is e.g. As/(As+Gs).

Repeat for all the positions.

[Eva_Maria]

Is there any programmes or tool to calculate this