ExRec

ExRec (Exclusion of Recombined DNA) is a Python pipeline that implements the four-gamete test to filter out recombined DNA sites from up to thousands of DNA sequence loci. The pipeline consists of five standalone applications: the first two convert folders of NEXUS or PHYLIP files into the standard input file for the main program that conducts the four-gamete filtering procedures. The pipeline outputs recombination-filtered data in concatenated NEXUS and PHYLIP formats and a tab-delimited table containing descriptive statistics for all loci and the results. This software also allows the user to output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach). Two other applications in the package convert the recombination-filtered data into single-locus NEXUS or PHYLIP files. The ExRec package can thus facilitate species delimitation, species tree, and historical demography studies by providing loci that better meet the no-recombination assumption in coalescent-based analyses.

Requirements and Installation

The ExRec pipeline runs under Python 3 without any dependencies. You can install ExRec by downloading the five applications from the ExRec Github page. Each script is run using the command line.

Documentation

A user’s manual is also included in the ExRec package. This document contains the instructions for using each of the five applications in ExRec as well as a tutorial that uses two sample data sets (also included in the package). Instructions on how to execute each application can also be found using the "help" command. On the command line, just cd to the folder containing the application you want to run, type in the following commands (choose one), and then type enter:

python3 Nexcombine.py help

python3 Phycombine.py help

python3 FGT.py help

python3 Nexsplit.py help

python3 Physplit.py help

License and Warranty

Please see the file "LICENSE" for details.