MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.

Systematic Biology
Fredrik RonquistJohn P Huelsenbeck

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...Continue Reading

References

Feb 1, 1993·Journal of Molecular Evolution·N Goldman
Jul 1, 1997·Molecular Biology and Evolution·Z Yang, B Rannala
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
May 24, 2001·Molecular Biology and Evolution·M A SuchardJ S Sinsheimer
Aug 29, 2001·Bioinformatics·J P Huelsenbeck, F Ronquist
Oct 25, 2002·Systematic Biology·Jeffrey L Thorne, Hirohisa Kishino
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Feb 13, 2004·Bioinformatics·Gautam AltekarFredrik Ronquist
Mar 23, 2004·Molecular Biology and Evolution·John P HuelsenbeckMichael E Alfaro
Mar 9, 2006·Systematic Biology·Nicolas Lartillot, Hervé Philippe
May 11, 2006·PLoS Biology·Alexei J DrummondAndrew Rambaut
Mar 30, 2007·Proceedings of the National Academy of Sciences of the United States of America·Scott V EdwardsDennis K Pearl
Sep 25, 2007·Molecular Biology and Evolution·Thomas LepageNicolas Lartillot
Feb 19, 2008·Systematic Biology·Clemens LaknerFredrik Ronquist
Apr 10, 2008·Molecular Biology and Evolution·David Posada
Jun 10, 2008·Journal of Theoretical Biology·Tanja Gernhard
Sep 5, 2008·Annual Review of Genomics and Human Genetics·Bruce Rannala, Ziheng Yang
Dec 8, 2009·Annual Review of Entomology·Fredrik Ronquist, Andrew R Deans
Dec 29, 2010·Systematic Biology·Wangang XieMing-Hui Chen
Apr 13, 2011·Molecular Biology and Evolution·Sebastian HöhnaTom Britton
Aug 11, 2011·Systematic Biology·Sebastian Höhna, Alexei J Drummond

❮ Previous
Next ❯

Citations

Sep 18, 2013·Nature Communications·Jon Jerlström-HultqvistStaffan G Svärd
Jul 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jean-François PombertPatrick J Keeling
Oct 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Qi ZhangWilfred A van der Donk
Nov 2, 2012·Proceedings of the National Academy of Sciences of the United States of America·Juan Carlos Villarreal, Susanne S Renner
Oct 9, 2013·Proceedings of the National Academy of Sciences of the United States of America·Juliane SchaerKai Matuschewski
Dec 20, 2013·Environmental Technology·Frank R BengelsdorfPeter Dürre
Jul 3, 2013·Vector Borne and Zoonotic Diseases·Antoine NougairedeRemi N Charrel
Mar 15, 2013·Molecular Biology of the Cell·Carme Gabernet-CastelloMark C Field
Jan 15, 2013·Genome Biology and Evolution·Chung-Shien WuYa-Yi Huang
Aug 21, 2013·Genome Biology and Evolution·Francesco ComandatoreMark Blaxter
Nov 28, 2013·Genome Biology and Evolution·Jacek KominekBarry L Williams
May 15, 2013·Integrative and Comparative Biology·Nadine RandelGáspár Jékely
Jul 19, 2013·Integrative and Comparative Biology·Walker Pett, Dennis V Lavrov
Mar 15, 2013·The Journal of Heredity·Sara J HansonJohn M Logsdon
Dec 13, 2012·Molecular Biology and Evolution·Chieh-Hsi WuAlexei J Drummond
Dec 4, 2012·Molecular Biology and Evolution·Dick RoelofsNico M van Straalen
Jan 23, 2013·Molecular Biology and Evolution·Jessica E Garb, Cheryl Y Hayashi
Feb 19, 2013·Molecular Biology and Evolution·Bui Quang MinhArndt von Haeseler
Feb 26, 2013·Molecular Biology and Evolution·Manuel GilMaria Anisimova
Mar 22, 2013·Molecular Biology and Evolution·Patrick C BrunnerBruce A McDonald
May 15, 2013·Molecular Biology and Evolution·Peng ZhangDavid C Cannatella
Jul 31, 2013·Molecular Biology and Evolution·Samuel V ScarpinoMark Kirkpatrick
Feb 22, 2013·Journal of the Royal Society, Interface·Carmel McDougallBernard M Degnan
Jul 19, 2013·Proceedings. Biological Sciences·Matt FriedmanMark R Graham
Sep 13, 2013·Proceedings. Biological Sciences·Eleftheria PalkopoulouJessica A Thomas
Jul 18, 2012·Antimicrobial Agents and Chemotherapy·Peter SpanogiannopoulosGerard D Wright

❮ Previous
Next ❯

Software Mentioned

Linux
FigTree
BEAGLE
MrBayes
Mac
BEST
PSRF
MPI

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Theoretical Biology
Tanja Stadler
Annual Review of Entomology
Fredrik Ronquist, Andrew R Deans
Systematic Biology
Alexandre Bouchard-CôtéMichael I Jordan
© 2021 Meta ULC. All rights reserved