<![CDATA[BOL: ExRec: Exclusion of Recombined DNA]]> https://bioinformaticsonline.com/bookmarks/view/44495/exrec-exclusion-of-recombined-dna? https://bioinformaticsonline.com/bookmarks/view/44495/exrec-exclusion-of-recombined-dna Wed, 27 Mar 2024 20:48:26 -0500 https://bioinformaticsonline.com/bookmarks/view/44495/exrec-exclusion-of-recombined-dna <![CDATA[ExRec: Exclusion of Recombined DNA]]> 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.

Link to the article: https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad174/7455250?searchresult=1

Link to the software:
https://github.com/Sammccarthypotter/ExRec

Address of the bookmark: https://github.com/Sammccarthypotter/ExRec

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