finding gene variation using Fasta files

Question

[Eva_Maria]

Hi

I have 50 genes and I want to find each genes variation(SNPs) in 400 genomes. All genes and genomes are in fasta format only. How is it possible?

Answer 1

[Zev.Kronenberg]

If you have the sequences aligned you can use:

https://github.com/zeeev/popFastaaa

samtools faidx MSA.fa
./SNP -s name  -f MSA.fa