MultiHit (FitMultiModel)
Does a codon alignment support changes at two or three positions in one event? MultiHit compares models that allow these substitutions with a model that allows only single hits.
Software
I build open-source software to study evolution from DNA sequences. Researchers can use these tools to compare genes across species and test how natural selection shapes proteins and viral genomes.
HyPhy methods
BUSTED-MH
Does a gene show evidence of episodic diversifying selection once multiple hits are allowed? This extension of BUSTED tests for selection while accounting for multinucleotide changes. BUSTED[S]-MH also allows synonymous rates to vary among sites.
Analysis workflows
2026 · Open source
AOC
Analysis of Orthologous Collections
A Snakemake workflow for comparing protein-coding genes across species. AOC automates codon-aware alignment, phylogenetic reconstruction, recombination detection, and HyPhy selection tests, then summarizes results across datasets.
2022 · Open source
RASCL
Rapid Assessment of Selection in CLades
A pipeline for testing how selection varies among clades in large sequence collections. RASCL automates phylogenetic and molecular selection analyses so researchers can compare evolutionary pressures across related lineages.