Hot Paper in Environment/Ecology

March 2014

Abstract: “Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.”

This 2012 report from Systematic Biology was cited 34 times in current journal articles indexed by Thomson Reuters during September-October 2013. No other paper published in the last two years and indexed by Thomson Reuters under the main heading of Environment/Ecology collected a higher number of citations during that two-month period. Prior to the most recent bimonthly count, citations to the report have accrued as follows, as tracked by Essential Science Indicators Hot Papers:

July-August 2013: 49 citations
May-June 2013: 40
March-April 2013: 40
January-February 2013: 38
November-December 2012: 20
September-October 2012: 12
July-August 2012: 2
May-June 2012: 2
January-February 2012: 6

Total citations to date: 243


SOURCE: Thomson Reuters Web of Science

The data and citation records included in this report are from Thomson Reuters Web of ScienceTM. Web of ScienceTM is a registered trademark of Thomson Reuters. All rights reserved.