πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

Protein evolution along phylogenetic histories under structurally constrained substitution models

(2013) Miguel Arenas et al.   BIOINFORMATICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Simulation of Molecular Data under Diverse Evolutionary Scenarios

(2012) Miguel Arenas   PLoS Computational Biology

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

(2011) Botond Sipos et al.   BMC BIOINFORMATICS

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

(2011) Ceiridwen J. Edwards et al.   CURRENT BIOLOGY

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

(2011) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

ALF—A Simulation Framework for Genome Evolution

(2011) Daniel A. Dalquen et al.   MOLECULAR BIOLOGY AND EVOLUTION

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

FLU, an amino acid substitution model for influenza proteins

(2010) Cuong Dang et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent Simulation of Intracodon Recombination

(2009) M. Arenas et al.   GENETICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

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

Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0

(2009) Cory L. Strope et al.   MOLECULAR BIOLOGY AND EVOLUTION

MtZoa: A general mitochondrial amino acid substitutions model for animal evolutionary studies

(2009) Omar Rota-Stabelli et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy

(2008) J. M. Brown et al.   BIOINFORMATICS

GENOMEPOP: A program to simulate genomes in populations

(2008) Antonio Carvajal-Rodríguez   BMC BIOINFORMATICS

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION