I'm in the process of comparing RNA-seq data from two fungal isolates by aligning against a refrance of the same species. I've performed the alignments using Tophat, and called variants using the GATK haplotype caller. I'd now like to estemate the Ka/Ks ratio for all the genes in my referance. However, the only programs I can find to calculate this require Fasta alignments. could anyone recomend a software or pipline that would get me what I need? I'd appriciate any advice.