VESPA: Viral Epidemiology Signature Pattern Analysis

Purpose: The VESPA program detects signature patterns (atypical amino acid or nucleotide residues) in a set of query sequences relative to a set of reference sequences.

Details: VESPA calculates the frequency of each amino acid (or nucleotide) at each position (column) in an alignment for the query and reference set, and selects the positions for which the most common character in the query set differs from that in the background set. The frequencies of characters at the distinguishing sites are also calculated. See Korber and Myers (1992).

How to use: Please read the VESPA instructions on how to use this program. If you have large sequence sets (over 100 sequences), please consider downloading a copy of Vespa to run on your own computer.