CoMuS: simulating coalescent histories and polymorphic data from multiple species

An early modern human from Romania with a recent Neanderthal ancestor

(2015) Qiaomei Fu et al.   NATURE

The diverse origins of the human gene pool

(2015) Svante Pääbo   NATURE REVIEWS GENETICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Demographic history of a recent invasion of house mice on the isolated Island of Gough

(2014) Melissa M. Gray et al.   MOLECULAR ECOLOGY

forqs: forward-in-time simulation of recombination, quantitative traits and selection

(2013) Darren Kessner et al.   BIOINFORMATICS

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Simulating gene trees under the multispecies coalescent and time-dependent migration

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

(2012) P. Duchen et al.   GENETICS

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

The Date of Interbreeding between Neandertals and Modern Humans

(2012) Sriram Sankararaman et al.   PLoS Genetics

Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster

(2011) S. S. Saminadin-Peter et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic evidence for archaic admixture in Africa

(2011) M. F. Hammer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simulating Trees with a Fixed Number of Extant Species

(2011) Tanja Stadler   SYSTEMATIC BIOLOGY

MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus

(2010) Gregory Ewing et al.   BIOINFORMATICS

Neanderthal genomics and the evolution of modern humans

(2010) J. P. Noonan   GENOME RESEARCH

msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis

(2010) P. PAVLIDIS et al.   Molecular Ecology Resources

Sampling Trees from Evolutionary Models

(2010) Klaas Hartmann et al.   SYSTEMATIC BIOLOGY

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Computing likelihoods for coalescents with multiple collisions in the infinitely many sites model

(2008) Matthias Birkner et al.   JOURNAL OF MATHEMATICAL BIOLOGY