Instructions for

This program is designed to perform phylogenetic analyses of sequence divergence and diversity. It first runs PHMYL to make an estimate of the maximum likelihood phylogeny, then runs PAUP to determine the most recent common ancestor (MRCA). After inputting the MRCA, the script runs PHMYL and PAUP again to get the distance matrix from which the genetic distances are parsed, and calculates the divergence and diversity.


  1. Sequence file: must be nucleotide sequence alignment in sequential nexus format.
  2. Outgroup file: a list containing only one field which lists all the names of the outgroup sequences.

  3. Ingroup file: a tab delimited table containing two fields. The first column contains the defined groups (grouped by sample time, or compartments, e.g.). The second column contains the names of sequences that belongs to those defined groups.

How to run

  1. You need to install PHYML and PAUP on your local computer and change the name of the PAUP executable file to "paup" (or create a symbolic link named "paup" to it in your path).
  2. Download the program to your local computer, and set it as executable by typing the following command in your working directory:

    chmod +x

  3. It is recommended that you make a subdirectory to hold input and output files for each run, because there will be a number of files created after running the program.

  4. In the subdirectory, type following command:

    perl ../ SequenceFile OutgroupFile IngroupFile