comparative-methods

R package: Evolutionary biology in R

R package to perform sensitivity analysis for comparative methods

Open Software for Teaching Evolutionary Biology at Multiple Scales Through Virtual Inquiries

Perform phylogenetic path analysis in R.

R package for evolutionary mapping of continuous traits

R package: joint models of chromosome number and binary traits

Supplementary R code for analyses in "Rates of passerine body plan evolution in time and space"

Independently maintained fork of l1ou for detecting evolutionary shifts and convergent regimes in comparative data.

Primitive functions for speeding up elements of a phylogenetic comparative workflow

Code and Figures for Souza Ferreira et al.

From-scratch molecular-phylogenetics algorithms in R — pairwise alignment, TN93 evolution simulation, UPGMA, Felsenstein likelihood, and independent contrasts, each with passing RUnit tests.

This directory contains code for the paper A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean. If you want to run this code, I recommend downloading this code and the data directory from Data Dryad.

Cattleya orchid hybridization over time and its phylogenetic signal, from RHS registration records (course write-up, 2025)