Instructions for

This program is designed to parse the output of LANL's HIV/SIV Sequence Locator Tool, and output AA or NA positions and genome NA positions for either nuclotide sequences or amino acid sequences.


  1. Output of Sequence Locator Tool saved as a text file.


  1. List of sequence index, organism, gene, AA or NA position, genome NA position and similarity.

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 ../ InputFile OutputFile