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Population Genomics

Recruit2Cloud

recruit2cloud1-0-2.py.zip
Author: Julio Cesar Ignacio-Espinoza
Last Revision: Sep 2012
Description: Recruit2cloud01.pl takes a series of genome reads, a reference genome, and a blastn of the reference genome (in that order) to generate a COV file. Each line in the COV file corresponds to all the bases found in that position after aligning the reads to the blastn output with muscle. The first-order option and file descriptor and option represent the file with the return-delimited list of genome reads. The second-order option and file descriptor and option represents the file with the reference genome. The third-order option and file descriptor and option represents the file with the blastn output of the reference genome.

plotSmall

plotsmall.pl.zip
Author: Julio Cesar Ignacio-Espinoza
Last Revision: Jan 2013
Description: plotSmall

SizeandLocation

sizeandlocation.pl.zip
Author: Julio Cesar Ignacio-Espinoza
Last Revision: Jan 2013
Description: SizeandLocation

DetectSynandNonSyn

detectsynandnonsyn.pl.zip
Author: Ann Gregory
Last Revision: Apr 2014
Description: From an alignment, this script will identify the total number of synonymous and nonsynonymous polymorphisms.

MKselection

mkselection.pl.zip
Author: Ann Gregory
Last Revision: Apr 2014
Description: Takes the input from detectsynandnonsyn.pl (above) and runs MK tests and determines if the gene is neutral, under positive selection or purifying selection.

remove_introns

remove_introns.pl.zip
Author: Ann Gregory
Last Revision: Apr 2014
Description: Using a list of identified pairs of genes with potential introns, this script removes and concatenates the two gene ends into the singe gene.

unique_fixed_polymorphisms

unique_fixed_polymorphisms.pl.zip
Author: Ann Gregory
Last Revision: Apr 2014
Description: Scans an alignment of population from two sites and looks for unique, fixed polymorphisms indicative of local adaptation.

bioinformatics/scripts/popgen.1398970188.txt.gz · Last modified: 2015/10/15 22:47 (external edit)
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