I have protein sequences from about 50 species which I want to align and observe/retrieve key (functionally interesting) sites. Apart from using Blast (blastp) to align sequences and view query anchored substitution patterns across the alignment, can somebody recommend to me another tool(s) which will align sequences and produce site-wise substitution mappings? Thanks.
use codeml from PAML package. You can check if the resulting positive selected sites (from codeml) fall within a domain or on an active site. I use python to plot the observed pos sites on uniprot annotations. Codeml models are bit difficult to understand initially but worth taking a look at the manual and if you are aligning distant related species then be aware of the alignment errors. A lot of literature already available on this. Hope this helps.