I have a large collection of human mitochondrial sequences and would like to characterise variable sites by whether they are coding or non-coding, if coding which codon position they are (i.e. 1st, 2nd or 3rd), and whether the variants present are synonymous or non-synonymous mutations.
Can anyone recommend some software that can do this by batch? Ideally I'd like to be able to just input a .fasta file and have it characterise all variable sites.
I have tried Mitomaster, but it is only telling me which sites are variable - not telling me anything about the nature of that variation.