Conservation Score Of Amino Acid Positions (2017)

Question

[bhffs01]

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.

[Asaf]

1. I'll always prefer an old tool which is still maintained over a new one.
2. You can look for papers citing old tools to see which new tools are out there.