Stars
Code from: Mitonuclear coevolution in bumblebees (Bombus): genomic signatures and its role in climatic niche adaptation
Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with…
biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute
A birth-death-hybridization based phylogenetic network simulator.
An R function to compute Concordance Factors from SNP datasets
Github repository for "Sequential trait evolution did not drive deep-time diversification in sharks" article, published in Evolution
Detection of evolutionary shifts in Ornstein-Uhlenbeck models
Script to run ancestral range estimation + biogeographic stochastic maps over a sample of phylogenetic trees.
Scripts relevant to Hahn & Hibbins D3 introgression statistic
Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
Automatically exported from code.google.com/p/figtree
An r package for Phylogenetic Diversity (PD) calculations in ecology, biogeography and conservation biology
Calculate Hybrid Index and Heterozygosity from SNP data
this will just get the ncbi db from genbank made
BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts
A Julia package for estimating phylogenetic networks from genomic data