fbaumdicker

goldfinder

Goldfinder detects gene co-occurrence and avoidance accounting for phylogenetic relationships

SpacerPlacer

ancestral reconstruction and likelihood analysis for CRISPR spacer arrays

AIMsetfinder

AIMsetfinder is a collection of Rscripts to identify sets of Ancestry Informative Markers (AIMs), that minimize the logloss error of a naive Bayes classifier.

panicmage

panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.

ML_in_pop_gen

adding-species-manuscript

manuscript materials for the adding species paper

applied_population_genetics

A textbook on population genetics

codebook

Source for The Good Research Code Handbook

erc-latex-template

LaTeX template for ERC proposals

lecture_notes

Lecture Notes on Computational and Mathematical Population Genetics

msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

msprime-1.0-paper

Publication describing msprime 1.0

pan-genome-analysis

Processing pipeline for pan-genome visulization and exploration

Phylogenetic-trees-python

This repository implements Phylogenetic Trees in Python

phylogenetics

A tutorial on making phylogenetic trees in python

SMBE-SGE-2019

Material for SMBE-SGE-2019 workshop

stdpopsim

A library of standard simulation models for msprime

Streptococcus-mutans-CRISPR-Spacers-Analysis

tangles