manuscript
This repository implements an automated system to write our collaborative manuscript, while tracking changes and contributions.
zol
zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
trisicell
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
poolgen
Quantitative and population genetics analyses of populations, pools, half-sib/full-sib families, and polyploids
phyloplace
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
dishtiny
DISHTINY: A Platform for Studying Open-Ended Evolutionary Transitions in Individuality
phageproteomictree
The phage proteomic tree was a breakthrough in evolution, taxonomy, and phylogenetics ... but nobody realized its global importance
py-ste
A Python package for evolving states under the Schrödinger equation using first-order Suzuki-Trotter and computing switching functions.
suzuki-trotter-evolver
A C++ header-only library for evolving states under the Schrödinger equation using first-order Suzuki-Trotter and computing switching functions.
ksrates
ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
hill_et_al_2023_iob_biogeography_analysis
Code and data to reproduce all analyses and figures in Hill et al 2023
islandevolution.github.io
Source code for the Island biology, diversification, genome evolution lab