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ITS2Rarefaction.py

calculates sample size versus specie diversity using blast results of ITS2 loci

calcFig4Martin2019.py

Creates a file for plotting that compares Fd and Recombination in comparison with Fig4 in Martin et al. 2019 https://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.2006288

divTime.py

uses algorithm in https://doi.org/10.1101/281881 to calculate div time between populations.

format_3PCLR.py

creates input file for use with 3P-CLR https://github.com/FerRacimo/3P-CLR

makeNegBed.py

make a bed file of coordinates not included in input. python makeNegBed.py 2L.gff 2L

popstats.py

Fork of https://github.com/pontussk/popstats

rho2cMMb.py

This script converts estimates of Rho from common programs into cMMb. Using a standard conversion of Ne or the methods of Booker et al. 2017 for wild mice https://doi.org/10.1534/genetics.117.300063. Can parse input from LDhelmet, LDJump, iSMC, ReLERNN.

stairs2ms.py

converts stairwayPlot output to ms command stairway2ms.py -i stairway.final.summary -L 1000

verfiy_discoalSims.py

Verify that runs of discoal for use with diploSHIC have proper number of simulations.