Haplotype-aware CNV analysis from single-cell RNA-seq

Interface to Open Tree of Life API

Functions for phylogenetic analyses

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

Detection of evolutionary shifts in Ornstein-Uhlenbeck models

I can haz all the phylogenies

Bacterial taxonomy construction and evaluation in R

The R interface to the Fish Tree of Life

htmlwidgets for phylocanvas

Bayesian inference of trait evolution under a “fossilized” Brownian motion.

An R Package for characterizing proteins using molecular evolution and phylogeny

Supplementary data and pipelines for analyzing genome gene content data and morphology to create various phylogenies.

Simulations of language evolution and phylogenetic/feature dynamics, as described in: "Kapur, Rhea and Phillip Rogers. 2020. Modeling language evolution and feature dynamics in a realistic geographic environment. 28th International Conference on Computational Linguistics (COLING 2020), Barcelona, Spain."

R package that estimates the error BEAST2 makes from a given phylogeny

Compute a phylogeny using EggNOG database

Creating Consensus Tree Figures with Ancestral State Estimations in BayesTraits

CGR package for phylogeny. Pipeline compare multiple whole genome sequences using alignment free approach Chaos Game Representation (CGR). CRG core function creates the frequencies object for each sequence which can be used to calculate distances among sequences.

App Shiny : Scalable visualization of groups within a hierarchical clustering from binary data matrix.

R package to visualize Synteny across biological species

Analysis scripts for Gortzia yakutica paper