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