HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

(2019) Daniel L Ayres et al.   SYSTEMATIC BIOLOGY

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Software Engineering for Computational Science: Past, Present, Future

(2018) Arne Johanson et al.   COMPUTING IN SCIENCE & ENGINEERING

Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

(2018) Steven Weaver et al.   MOLECULAR BIOLOGY AND EVOLUTION

The State of Software for Evolutionary Biology

(2018) Diego Darriba et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Cloud computing for genomic data analysis and collaboration

(2018) Ben Langmead et al.   NATURE REVIEWS GENETICS

Relative evolutionary rate inference in HyPhy with LEISR

(2018) Stephanie J. Spielman et al.   PeerJ

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Gene-Wide Identification of Episodic Selection

(2015) Ben Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

Evolutionary Fingerprinting of Genes

(2009) S. L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parsing Social Network Survey Data from Hidden Populations Using Stochastic Context-Free Grammars

(2009) Art F. Y. Poon et al.   PLoS One