cactus-snakemake
Generate and manipulate whole genome alignments efficiently. Cactus is a tool for aligning multiple genomes, outputting HAL files. These Snakemake workflows allow you to run Cactus efficiently on a cluster to generate an manipulate whole genome alignments. There is an additional workflow for Minigraph-cactus to infer pangenomes. See tutorials for these pipelines here.

degenotate
Annotate the degeneracy of coding sites in a genome and extract coding sequences of specified degeneracy. Also counts synonymous and nonysnonymous changes within and between populations to perform a basic MK test. Included in the snpArcher variant calling workflow.

PhyloAcc
Substitution rate shifts in non-coding DNA. A Bayesian framework to estimate substitution rates in non-coding DNA elements, developed in Hu et al. 2019. Version 2 now accounts for phylogenetic discordance.

pseudo-it
Reference-based genome assembly with iterative read mapping to alleviate reference bias. Software developed in the Good lab to reduce reference bias in reference-based genome assembly using an iterative mapping process to generate pseudo-genomes.

Referee
Reference assembly quality scores. Using genotype likelihoods from reads mapped back to an assembly, Referee assigns a quality score to every position of that assembly. Developed in Thomas and Hahn 2019.

GRAMPA
Gene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis. Software to identify polyploidy events given a species tree and a set of gene trees. Can count duplications and losses in the presence of polyploidy and differentiate between auto- and allopolyploidy events. Developed in Thomas et al. 2017.

CAFE
Computational Analysis of Gene Family Evolution. Software developed in the Hahn lab to estimate rates of gene family evolution and reconstruct ancestral gene counts. I contributed version 3.

GWCT
Genome-Wide Convergence Tester. These scripts and earlier versions of them were used in Foote et al. 2015, Thomas and Hahn 2015, and Thomas et al. 2017 to count convergent and divergent substitutions in a phylogeny. No longer maintained.

CORE
COde for Romps in Evolutionary data. My personal scripts and libraries for manipulating sequence data, phylogenetic trees, and other things. Best acronym.

ArthroFam.org
A website I built to browse phylogenetic, gene family, and protein domain results of 76 arthropod species as part of the i5K pilot project.

Macaque CNVs
Code and data used to produce the figures in our rhesus macaque CNV paper.

Owl monkey mutations - Github
A markdown document to accompany our paper on mutation rates in owl monkeys. Goes through our analyses and provides code for reproducible figures.

Drosophila 25 species phylogeny
A FigShare micro-publication of the 25 species Drosophila phylogeny that was used to study gene families across the genus, in particular salivary glue genes.

Birds-of-paradise gene families
Results of gene family analyses in several species of birds-of-paradise. Paper.

Harvard Informatics
My current group, with Tim Sackton.

Good lab
My postdoc advisor at the University of Montana.

Hahn lab
My PhD advisor at Indiana University.

Kihara lab
My undergrad lab at Purdue University.