I am looking to calculate per position conservation scores for multiple alignments of amino acids. I have fasta files for each exon in hg19 aligned to 46 primates, mammals, and vertebrates (the 46 way ucsc alignment).
I've seen this question be asked a few times but quite a long time ago (> 4~5 years.) I'm wondering if there are any newer tools to solve this problem. There is plenty for nucleotide positions but I need AA specifically.