Hi,

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 estiimate the Ka/Ks ratio for all the genes in my reference. However, the only programs I can find to calculate this require Fasta alignments. could anyone recommend a software or pipline that would get me what I need? I'd appreciate any advice.

Thanks