stevemussmann
I study native fishes of the Western US using RADseq and other NGS technologies.
U.S. Fish & Wildlife ServiceLongview, WA
Pinned Repositories
admixturePipeline
A pipeline that accepts a VCF file to run through Admixture
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
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
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
file_converters
A collection of file format converters to prepare input for several popular phylogenetic and population genetics software packages.
museum_collections_website
This is a website I wrote to manage museum collections for the Ichthyology course at UARK
StreamTree_arcpy
A project using Python (arcpy) to analyze genetic diversity of aquatic organisms over a stream network
stevemussmann's Repositories
stevemussmann/admixturePipeline
A pipeline that accepts a VCF file to run through Admixture
stevemussmann/BayesAss3-SNPs
Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
stevemussmann/Comp-D_MPI
A program for comprehensive computation of D-statistics and population summaries using MPI
stevemussmann/file_converters
A collection of file format converters to prepare input for several popular phylogenetic and population genetics software packages.
stevemussmann/BA3-SNPS-autotune
Python code for automatically tuning mixing parameters in BayesAss3
stevemussmann/cpm_genome_assembly
Scripts used for assembly of the Colorado Pikeminnow (Ptychocheilus lucius) genome
stevemussmann/GTseqTools
Program for filtering GTseq genotype data and converting to various file formats
stevemussmann/StreamTree_arcpy
A project using Python (arcpy) to analyze genetic diversity of aquatic organisms over a stream network
stevemussmann/ddrad_tools
My implementation of FRAGMATIC: a tool for optimizing ddRADseq projects
stevemussmann/chimaeraCheck
stevemussmann/DENdriscape
Code for riverscape genetics - examining patterns of genetic differentiation in dendritic networks
stevemussmann/dge_scripts
Scripts for differential gene expression analysis
stevemussmann/fastStructure3
Python3 compatible update of Anil Raj's fastStructure
stevemussmann/genepopParse
Scripts for parsing output of Genepop
stevemussmann/GTscore
Pipeline for GTseq genotyping and quality control
stevemussmann/gtseqMAF
Python program for calculating minor allele frequency (MAF) both globally and by population
stevemussmann/gtseqQAQC
Compare genotypes from two GTseq sequencing runs
stevemussmann/gtseqSim
Simulate genotype data based on allele frequencies
stevemussmann/HybridAgreement
Scripts for comparing hybrid classification results from Snapclust and NewHybrids
stevemussmann/hybriddetective
stevemussmann/HybridizationScripts
stevemussmann/kraken2
The second version of the Kraken taxonomic sequence classification system
stevemussmann/p12automation
stevemussmann/parentage_scripts
A collection of scripts useful in conducting parentage and relatedness analyses. These are mostly converters for popular parentage and relatedness software.
stevemussmann/phylip2introgress
stevemussmann/R_scripts
R scripts used for analyzing genetic data
stevemussmann/recom-sim
Hybrid simulation tool
stevemussmann/Rscripts-fineRADstructure
stevemussmann/templates
stevemussmann/utilities
random scripts for processing genetic data that don't fit in my other repositories