I am looking for a command line program that can perform the HKA test on fasta files. I have seen that programs like dnaSP are available, but I don't believe they are command line. Maybe I've missed a few, but I can't seem to find anything to calculate these values on a computing cluster.

I would also like to compute MacDonald Kreitman values on the same sequences, but I do know that packages like Popgenome for R are available.

Thanks.