A repository of scripts used in Beringia pop gen study. Versions as used in submitted manuscript.
find_chrom.py Using BLASTn output (as an .xml), find loci mapped to a specific locus (user-specified) and create an output file excluding them. Initially written to remove Z-linked loci from UCE datasets. Requirements: BioPython, phyluce
biallelicSNPs.py Find non-biallelic SNPs and create a new vcf file without them. Necessary for preparing files for analyses limited to biallelic data.
randomSNP.py When thinning to 1 SNP per locus, select a random SNP (rather than just the first SNP listed).
bootstrap_dadi.py resamples individuals (with replacement) to create bootstrapped datasets and runs each a user-specified number of times with DaDi.
ngapi_dadi.py resamples individuals without replacement within a given subsampled dataset, and similar to bootstrap_dadi.py, runs each a specified number of times in DaDi. Used for investigating impact of low sample size on estimates of demographic parameters.