README

This repo contains visualization and analysis scripts that I've written to help me perform
phylogenomic analyses. Almost all are written in Perl. Some require the Bioperl package.

Scripts that require the Bioperl package will either call the Bio package directly or require
subfunctions that are in the file bioperl_subfuncs.pl. It might be easiest if you include
this directory in your $PERL5LIB path so that the various subfunction files are easy for
the interpreter to find.

CircleGraph.pm is an object-oriented package that makes it easier to draw graphs along
a circle. It makes postscript objects and uses the Postscript::Simple package.

subfuncs.pl is a random hodgepodge of utility functions. As I write more of them, I may
move some to more specific subfunction files to reduce overhead.

bioperl_subfuncs.pl has helper functions that require Bioperl packages.

circlegraph.pl has helper functions that draw specific kinds of circular graphs.

The subdirs contain scripts for various tasks:
- analysis: scripts that perform various analyses on datasets.
    introgression: scripts to calculate statistics for introgression analysis.
    selection: scripts that use Bioperl, PAML, HyPhy to analyze selection on genes.
- converting: scripts to convert files from one format to another or to combine files
  in various ways.
- filtering: scripts that reduce complexity.
- parsing: uses Bioperl to slice and dice sequence files in various ways.
- plastome: scripts that take input about the plastome and draw circle graphs to
  represent that data.
- reporting: scripts that take vcf or sequence files and report statistics about them.