This page proposes a selection of tools to analyse and compare protein sequences and protein coding sequences.
PATH
This tool addresses the problem of finding distant protein homologies where the divergence is the result of frameshift mutations and substitutions.
Protea
This software analyses families of short conserved DNA sequence, and determines whether they are coding protein sequences. It is also able to predict the reading frame.
ReBlosum
The Rectangular BLOSUM matrices give scores to compare amino acid groups from different alphabets.