Steve Mussmann's repositories
admixturePipeline
A pipeline that accepts a VCF file to run through Admixture
BayesAss3-SNPs
Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
Comp-D_MPI
A program for comprehensive computation of D-statistics and population summaries using MPI
file_converters
A collection of file format converters to prepare input for several popular phylogenetic and population genetics software packages.
BA3-SNPS-autotune
Python code for automatically tuning mixing parameters in BayesAss3
cpm_genome_assembly
Scripts used for assembly of the Colorado Pikeminnow (Ptychocheilus lucius) genome
GTseqTools
Program for filtering GTseq genotype data and converting to various file formats
StreamTree_arcpy
A project using Python (arcpy) to analyze genetic diversity of aquatic organisms over a stream network
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
fastStructure3
Python3 compatible update of Anil Raj's fastStructure
genepopParse
Scripts for parsing output of Genepop
GTscore
Pipeline for GTseq genotyping and quality control
gtseqMAF
Python program for calculating minor allele frequency (MAF) both globally and by population
gtseqQAQC
Compare genotypes from two GTseq sequencing runs
gtseqSim
Simulate genotype data based on allele frequencies
HybridAgreement
Scripts for comparing hybrid classification results from Snapclust and NewHybrids
kraken2
The second version of the Kraken taxonomic sequence classification system
parentage_scripts
A collection of scripts useful in conducting parentage and relatedness analyses. These are mostly converters for popular parentage and relatedness software.
recom-sim
Hybrid simulation tool
utilities
random scripts for processing genetic data that don't fit in my other repositories