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admixture_cv_sum

[DEPRECATED] Summarizes the output of cross-validation values for multiple runs of admixture

admixturepipeline

A pipeline that accepts a VCF file to run through Admixture

astral_pipeline

A pipeline for processing a pyRAD .loci file by performing naive binning, running RAxML, and directing the output into ASTRAL

ba3-snps-autotune

Python code for automatically tuning mixing parameters in BayesAss3

bayesass3-snps

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets

bayesass_sum

Code to summarize output of using bayesass to conduct a sliding-window approach to examining migration over a stream network

bioconda-recipes

Conda recipes for the bioconda channel.

breadth-first-search_ai

working independently through assignments for an AI course

checkgff

Check a GFF file to see if a sequence falls within the coordinates of a gene

chimaeracheck

clockstar_format

Takes output of partition modeling in IQtree and formats it for input to ClockstaR

comp-d

A program for comprehensive computation of D-statistics and population summaries (Serial version)

comp-d_mpi

A program for comprehensive computation of D-statistics and population summaries using MPI

compdparse

Scripts for parsing output from compD

cpm_genome_assembly

Scripts used for assembly of the Colorado Pikeminnow (Ptychocheilus lucius) genome

ddrad_tools

My implementation of FRAGMATIC: a tool for optimizing ddRADseq projects

dendriscape

Code for riverscape genetics - examining patterns of genetic differentiation in dendritic networks

dge_scripts

Scripts for differential gene expression analysis

distruct-rerun

[DEPRECATED] Python code to prepare data to rerun distruct based upon the major clusters found by clumpak

examl_pipeline

Pipeline for running ExaML

faststructure3

Python3 compatible update of Anil Raj's fastStructure

file_converters

A collection of file format converters to prepare input for several popular phylogenetic and population genetics software packages.

fstoutlierconcordance

Compare outputs of BayeScan and Lositan to identify loci detected to be under selection by both methods.

genemapperparser

Tools for parsing genemapper output

genepopparse

Scripts for parsing output of Genepop

gtscore

Pipeline for GTseq genotyping and quality control

gtseq-pipeline

A series of perl and python scripts for generating genotypes from NGS fastq files from GTseq library sequencing.

gtseqmaf

Python program for calculating minor allele frequency (MAF) both globally and by population

gtseqqaqc

Compare genotypes from two GTseq sequencing runs

gtseqtools

Program for filtering GTseq genotype data and converting to various file formats