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
clipkit
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
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.
orthofisher
a broadly applicable tool for automated gene identification and retrieval
LTRpred
LTRpred: de novo annotation of intact retrotransposons - Published in JOSS (2020)
dishtiny
DISHTINY: A Platform for Studying Open-Ended Evolutionary Transitions in Individuality
paleobuddy
paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R.
epistasis
A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
https://github.com/cjabradshaw/coelacanthevolution
Analyses of coelacanth morphometrics, disparity, phylogeny, and rate of evolution
https://github.com/chenyangkang/bird_phylogeny
Bird (avian) phylogenetic tree with bird pictures
https://github.com/charlesrocabert/metevolsim
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
coevolve
coevolve R package for Bayesian generalized dynamic phylogenetic models using Stan
suzuki-trotter-evolver
A C++ header-only library for evolving states under the Schrödinger equation using first-order Suzuki-Trotter and computing switching functions.
https://github.com/compevol/beast2
Bayesian Evolutionary Analysis by Sampling Trees
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.
ksrates
ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
hill_et_al_2023_iob_biogeography_analysis
Code and data to reproduce all analyses and figures in Hill et al 2023
SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
islandevolution.github.io
Source code for the Island biology, diversification, genome evolution lab
traitblender
Blender addon for simulating raw datasets under known evolutionary models
https://github.com/dalmolingroup/orthoguide
A web application for evolutionary rooting of genes