Instructions for CountAAFreq.pl
This program is designed to calculate amino acid frequency at each position of a set of aligned amino acid sequences.
- Amino acid sequence alignment file in Nexus format.
- 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.
- 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.
- Tab delimited table of amino acid frequency, the most and second most frequency amino acids and their frequencies at each position.
How to run
- Download CountAAFreq.pl to your local computer, and set it as executable by typing the following command in your working directory:
chmod +x CountAAFreq.pl
Create a subdirectory in your working directory to hold input files and output files. In the subdirectory, type following command:
perl ../CountAAFreq.pl AASeqAlignFile OtputFile GapCutoff FrequencyCutoff