Instructions for

This program is designed to calculate amino acid divergence window by window that user defined from a set of aligned amino acid sequences.


  1. Amino acid sequence alignment file in fasta.
  2. Window size (default: 9 amino acids).
  3. Window stride size (default: 1 amino acids).


  1. Tab delimited table of divergence in each window.

How to run

  1. Download to your computer, expand it and type the following command in your working directory:

    perl -ia AASeqAlignFile -od OtputFile -ws WindowSize -ss StrideSize