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gila_simulations

My top secret repository for my SLiM scripts >:)

haplotools

Python scripts to create input files for haplotype reconstruction in Phase, parse outputs, and perform some other manipulations with haplotypes/ diplotypes

hisse

Hidden State Speciation and Extinction

htslib

C library for high-throughput sequencing data formats

jiachen_dissertation

lithops

A multi-cloud framework for big data analytics and embarrassingly parallel jobs, that provides an universal API for building parallel applications in the cloud ☁️🚀

locator

deep learning prediction of geographic location from individual genome sequences

makecompd

makes large number of test files for Steve Mussmann's Comp-D d-statistic program. Can randomly select individuals, or use provided weights file.

makepopmap

Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

mantel

Python implementation of the Mantel test, a significance test of the correlation between two distance matrices

mcpopsim

Forward-time Markov Chain DNA sequence evolution simulator which alows sequences to be simulated along a fixed-N taxon tree according to a user defined scenario. This project was a part of a summer C++ course taken in 2015, and has not been thoroughly vetted.

misc_scripts

mpe_impute_2022

Supplementary materials for Chafin and Martin 2022

mpi-bucky

A parallel implementation of BUCKy using OpenMPI message passing interface

mrbait

Pipeline for universal design of target-enrichment probes from various sources of genomic data.

multiwaver_snakemake_workflow

Snakemake workflow for running MultiWaver2.0 given data tables of ancestry assignments and a genetic map from which to interpolate genetic distances from physical distances

ncbi-tax-summary

Given a table having a column containing NCBI accession numbers of GenInfo (GI) IDs (i.e., from tabular blast output), generates tables summarizing taxonomic representation at various ranks

newhyb_pipeline

open-science_proposals

Repository for me to share my funded and failed past proposals

pbs_scripts

Batch scripts for random things on AHPCC Trestles

pg-sui

Python machine learining API to impute missing genotypes from population genomic data

phylonetworks.jl

A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks

phylo_impute

polyrad_scripts

Scripts for working with inputs and outputs of polyRAD genotyper

pyrad_demultiplex_workdir

Template directory for batches of pyRAD demultiplex runs

pyvolve

Python library to simulate evolutionary sequence data

resistancega

Optimize resistance surfaces using Genetic Algorithms

resistancega_hpc_pipeline

Nextflow pipeline for running ResistanceGA's (R package) all_comb() on HPC

resistnet

Code for fitting environmental resistance models in spatial networks (e.g., riverscapes)

r_scripts

Various R scripts, generally without documentation and with hard-coded values :(