/Recombination-detection-pipeline-for-large-gene-families

Automates detection of recombination events in large gene families (works with gene families with >1000 genes)

Primary LanguagePerl

Recombination-detection-pipeline-for-large-gene-families

This set of PERL scripts automates detection of recombination events in large gene families.

This computation pipeline is reported in the following article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020489/

It was tested with
(1) T. cruzi trans-sialidase gene family (3209 genes with an average length of 1.5kb)
(2) T. cruzi MASP gene family (1032 genes)
(3) T. cruzi Mucin gene family (661 genes)

PERL script #1,#3,#4,#6 runs in Linux , and #2,#5 runs in window environment

This set of PERL scripts is in active development. Please direct any questions to github.com/duopeng

Required software:

NCBI BLAST 2.2.29+

clustalw2

RDP4