A jupyter notebook tutorial for making high-quality barplot figures from population structure analyses (Admixture, Structure) with Python & Pandas.

A Python tool for calculating sexual size dimorphism indices from body size data. Performs permutation tests to determine statistically significant sexual dimorphism.

An accessible and flexible tool for fitting demographic models with moments using custom or published models (available here) and conducting goodness of fit tests.

A tool for summarizing and visualizing metrics for sequence alignment files in phylip format. Designed to execute on a directory containing up to several thousand phylip files.

Convert PHYLUCE genome-extracted UCE sequence data to GenBank style fasta labeling that is compatible with SuperCRUNCH.

An automated workflow for processing ddRADseq data using Stacks v2.4. Starts with sequencer files, and ends with various input files for phylogenetic/phylogeography programs.

Scripts to help automate various phylogenetic or phylogeography programs (Admixture, RAxML, CLUMPP + DISTRUCT). Also includes a script for replacing sample or taxon names in input files.

A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.

A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.

A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

Taxonomy-guided multiple sequence alignment for difficult genes, including 12S and 16S mitochondrial rRNA.

Convert a set of phased alignment fasta files into a Structure input file. Intended to work with seq-capture and ddRADseq datasets.

A 1:1 comparison of my academic CV and industry resume, with some tips on making an industry resume.

Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at the Jackson Laboratory.

Hidden state speciation and extinction analyses of sexual dichromatism in Afrobatrachian frogs.

A script to filter phylip alignments by minimum bp length, missing data across individual sequence or whole alignment, with subsequent trimming function to reduce missing data.

Scripts for pruning taxa from tree files, performing Robinson-Foulds comparisons, and calculating node-support indices. All intended for a directory of tree files, rather than a single tree.

Script to help calculate coverage of a sample or contigs within a sample for sequence capture data sets.