Inferring whole-genome histories in large population datasets

A method for genome-wide genealogy estimation for thousands of samples

(2019) Leo Speidel et al.   NATURE GENETICS

Estimating Time to the Common Ancestor for a Beneficial Allele

(2018) Joel Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Haplotype matching in large cohorts using the Li and Stephens model

(2018) Gerton Lunter   BIOINFORMATICS

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

(2018) Benjamin C Haller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes

(2018) Benjamin C. Haller et al.   Molecular Ecology Resources

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Efficient pedigree recording for fast population genetics simulation

(2018) Jerome Kelleher et al.   PLoS Computational Biology

treespace : Statistical exploration of landscapes of phylogenetic trees

(2017) Thibaut Jombart et al.   Molecular Ecology Resources

Genealogies: Pedigrees and Phylogenies are Reticulating Networks Not Just Divergent Trees

(2016) David A. Morrison   Evolutionary Biology

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution

(2016) Michelle Kendall et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

(2016) Jerome Kelleher et al.   PLoS Computational Biology

Estimating the Ages of Selection Signals from Different Epochs in Human History

(2015) Shigeki Nakagome et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring the age of a fixed beneficial allele

(2015) Louise Ormond et al.   MOLECULAR ECOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

(2014) R. Durbin   BIOINFORMATICS

Genome-Wide Inference of Ancestral Recombination Graphs

(2014) Matthew D. Rasmussen et al.   PLoS Genetics

ACG: rapid inference of population history from recombining nucleotide sequences

(2013) Brendan D O'Fallon   BMC BIOINFORMATICS

GraphML specializations to codify ancestral recombinant graphs

(2013) James R. McGill et al.   Frontiers in Genetics

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Trees and networks before and after Darwin

(2009) Mark A Ragan   Biology Direct

Extended Newick: it is time for a standard representation of phylogenetic networks

(2009) Gabriel Cardona et al.   BMC BIOINFORMATICS

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns

(2008) Laxmi Parida et al.   JOURNAL OF COMPUTATIONAL BIOLOGY