BEAST (Bayesian Evolutionary Analysis by Sampling Trees)

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Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. (2012, methodology): “PartitionFinder implements almost all of the models of nucleotide evolution included in the most commonly used phylogenetic tree estimation programs such as PhyML (Guindon et al. 2010), RaxML (Stamatakis 2006), MrBayes (Ronquist and Huelsenbeck 2003), and BEAST (Drummond and Rambaut 2007).”
Biogeographical diversification of mainland Asian Dendrobium (Orchidaceae) and its implications for the historical dynamics of evergreen broad‐leaved forests (2016, neutral): “5 (Rambaut & Drummond, 2007).”
Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement (2012, methodology): “Ages of clades were inferred using BEAST, version 1.6.1 (Drummond et al ., 2006; Drummond & Rambaut, 2007).”
Testing geological models of evolution of the Isthmus of Panama in a phylogenetic framework (2013, neutral): “, 2006; Drummond & Rambaut, 2007).”
Bayesian Phylogenetics with BEAUti and the BEAST 1.7 (2012, methodology): “Here, we present a major new version of the molecular evolutionary software package Bayesian Evolutionary Analysis by Sampling Trees (BEAST), updated to version 1.7, and representing a significant software advance over that previously described (Drummond and Rambaut 2007).”