Instructions for

This program is designed to calculate amino acid frequency at each position of a set of aligned amino acid sequences.


  1. Amino acid sequence alignment file in Nexus format.
  2. Cutoff value for gap fraction at each position (0 - 1). If the gap percentage is beyond the cutoff value at a position, the amino acid frequency is not calculated for that position.
  3. Cutoff value for amino acid frequency (0 - 1). If the most frequenct (or the sum of the most and second most frequenct) amino acid is above the cutoff value in a position, the most frequenct (or both of the most and second most frequenct) amino acid, and the frequency is written to the output.


  1. Tab delimited table of amino acid frequency, the most and second most frequency amino acids and their frequencies at each position.

How to run

  1. Download to your local computer, and set it as executable by typing the following command in your working directory:

    chmod +x

  2. Create a subdirectory in your working directory to hold input files and output files. In the subdirectory, type following command:

    perl ../ AASeqAlignFile OtputFile GapCutoff FrequencyCutoff