MRBAYES: Bayesian inference of phylogenetic trees

By John P. Huelsenbeck, Fredrik Ronquist. Bioinform., 2001

21,757 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/465ecac8eddd2c362f0e10de2583a62a1a7c371a

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Artificial Intelligence

1. Alexei J. Drummond
2. Jasper A. Vrugt
3. Josh Tenenbaum
4. T. Griffiths
5. John P. Huelsenbeck
6. Nicolas Lartillot
7. Hervé Philippe
8. Christian P. Robert

In Genetics

1. Ziheng Yang
2. Alexei J. Drummond
3. John J. Wiens
4. Andrew Rambaut
5. Olivier Gascuel
6. Marc A. Suchard
7. Alexandros Stamatakis
8. Fredrik Ronquist

In Molecular Biology

1. Ziheng Yang
2. Alexei J. Drummond
3. Alexandros Stamatakis
4. John J. Wiens
5. K. D. Hyde
6. Olivier Gascuel
7. J. Doyle
8. John P. Huelsenbeck

Citations in the corpus

• Phylogenetic Relationships in Fagales Based on DNA Sequences from Three Genomes (2004, methodology): “Bayesian inference (BI) was conducted using MrBayes version 2.0 (Huelsenbeck and Ronquist 2001).”
• Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference (2002, methodology): “, 1953; Hastings, 1970) has been successfully used to approximate the posterior probability distribution of trees (Yang and Rannala, 1997; Larget and Simon, 1999; Huelsenbeck and Ronquist, 2001).”
• The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence (2013, methodology): “1.2 (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003) and posterior probabilities were calculated using a MCMC sampling approach.”
• Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae) (2009, methodology): “For Bayesian phylogenetic analyses (Rannala & Yang, 1996) we used MrBayes version 3.2.1 ( Huelsenbeck & Ronquist, 2001 ).”
• Integrative taxonomy identifies new (and old) species in the Lasioglossum (Dialictus) tegulare (Robertson) species group (Hymenoptera, Halictidae) (2009, methodology): “A Bayesian phylogenetic analysis was performed using MrBayes v. 3.1.2 (Huelsenbeck & Ronquist 2001) on the DNA barcode dataset.”
• Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming (2011, methodology): “1.2 (Huelsenbeck and Ronquist, 2001), starting with a random tree, run two million generations in four chains and with a burn-in of 2000 generations, using parameters similar to the ML method.”
• Phylogeography of Ptychadena mascareniensis suggests transoceanic dispersal in a widespread African‐Malagasy frog lineage (2004, methodology): “Bayesian posterior probabilities were calculated using MrBayes, version 2.01 (Huelsenbeck & Ronquist, 2001) 594 Journal of Biogeography 31, 593–601, ª 2004 Blackwell Publishing Ltd under a GTR substitution model with parameters estimated from the data.”
• Accelerating Markov Chain Monte Carlo Simulation by Differential Evolution with Self-Adaptive Randomized Subspace Sampling (2009, methodology): “Ever since, the method has found widespread use for sampling from posterior distributions in many fields of study ranging from physics and chemistry, to finance, economics, genetics, statistical inference, hydrology, biology and bioinformatics [3, 4, 5, 6,7,8,9,10,11,12].”
• The name game: morpho‐molecular species boundaries in the genus Psammocora (Cnidaria, Scleractinia) (2010, methodology): “Phylogenetic relationships were inferred under Bayesian (Huelsenbeck et al., 2001; Huelsenbeck & Ronquist, 2001) and maximum likelihood approaches.”