GenPhyloData: realistic simulation of gene family evolution

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

(2013) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

DLRS: gene tree evolution in light of a species tree

(2012) Joel Sjöstrand et al.   BIOINFORMATICS

ALF—A Simulation Framework for Genome Evolution

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

Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence

(2011) Martin Linder et al.   SYSTEMATIC BIOLOGY

Simulating Trees with a Fixed Number of Extant Species

(2011) Tanja Stadler   SYSTEMATIC BIOLOGY

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Probabilistic Orthology Analysis

(2009) Bengt Sennblad et al.   SYSTEMATIC BIOLOGY