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Items: 1 to 20 of 70


Reply to Nakov et al.: Model choice requires biological insight when studying the ancestral habitat of photosynthetic eukaryotes.

Sánchez-Baracaldo P, Bianchini G, Huelsenbeck JP, Raven JA, Pisani D, Knoll AH.

Proc Natl Acad Sci U S A. 2017 Dec 5. pii: 201717417. doi: 10.1073/pnas.1717417114. [Epub ahead of print] No abstract available.


Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures.

Moore BR, Höhna S, May MR, Rannala B, Huelsenbeck JP.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9569-74. doi: 10.1073/pnas.1518659113. Epub 2016 Aug 10.


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

Höhna S, Landis MJ, Heath TA, Boussau B, Lartillot N, Moore BR, Huelsenbeck JP, Ronquist F.

Syst Biol. 2016 Jul;65(4):726-36. doi: 10.1093/sysbio/syw021. Epub 2016 May 28.


Strepsiptera, phylogenomics and the long branch attraction problem.

Boussau B, Walton Z, Delgado JA, Collantes F, Beani L, Stewart IJ, Cameron SA, Whitfield JB, Johnston JS, Holland PW, Bachtrog D, Kathirithamby J, Huelsenbeck JP.

PLoS One. 2014 Oct 1;9(10):e107709. doi: 10.1371/journal.pone.0107709. eCollection 2014.


The fossilized birth-death process for coherent calibration of divergence-time estimates.

Heath TA, Huelsenbeck JP, Stadler T.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E2957-66. doi: 10.1073/pnas.1319091111. Epub 2014 Jul 9.


Probabilistic graphical model representation in phylogenetics.

Höhna S, Heath TA, Boussau B, Landis MJ, Ronquist F, Huelsenbeck JP.

Syst Biol. 2014 Sep;63(5):753-71. doi: 10.1093/sysbio/syu039. Epub 2014 Jun 20.


A phylogenetic model for the detection of epistatic interactions.

Nasrallah CA, Huelsenbeck JP.

Mol Biol Evol. 2013 Sep;30(9):2197-208. doi: 10.1093/molbev/mst108. Epub 2013 Jun 6.


Bayesian analysis of biogeography when the number of areas is large.

Landis MJ, Matzke NJ, Moore BR, Huelsenbeck JP.

Syst Biol. 2013 Nov;62(6):789-804. doi: 10.1093/sysbio/syt040. Epub 2013 Jun 4.


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

Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.

Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029. Epub 2012 Feb 22.


A dirichlet process prior for estimating lineage-specific substitution rates.

Heath TA, Holder MT, Huelsenbeck JP.

Mol Biol Evol. 2012 Mar;29(3):939-55. doi: 10.1093/molbev/msr255. Epub 2011 Nov 2.


BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100. Epub 2011 Oct 1.


Structurama: bayesian inference of population structure.

Huelsenbeck JP, Andolfatto P, Huelsenbeck ET.

Evol Bioinform Online. 2011;7:55-9. doi: 10.4137/EBO.S6761. Epub 2011 Jun 2.


Biologically inspired phylogenetic models strongly outperform the no common mechanism model.

Huelsenbeck JP, Alfaro ME, Suchard MA.

Syst Biol. 2011 Mar;60(2):225-32. doi: 10.1093/sysbio/syq089. Epub 2011 Jan 20.


Quantifying the impact of dependent evolution among sites in phylogenetic inference.

Nasrallah CA, Mathews DH, Huelsenbeck JP.

Syst Biol. 2011 Jan;60(1):60-73. doi: 10.1093/sysbio/syq074. Epub 2010 Nov 15.


Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence.

Bollback JP, Huelsenbeck JP.

Genetics. 2009 Jan;181(1):225-34. doi: 10.1534/genetics.107.085225. Epub 2008 Nov 10.


Statistical assignment of DNA sequences using Bayesian phylogenetics.

Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R.

Syst Biol. 2008 Oct;57(5):750-7. doi: 10.1080/10635150802422316.


Bayesian analysis of amino acid substitution models.

Huelsenbeck JP, Joyce P, Lakner C, Ronquist F.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3941-53. doi: 10.1098/rstb.2008.0175.


A Bayesian perspective on a non-parsimonious parsimony model.

Huelsenbeck JP, Ané C, Larget B, Ronquist F.

Syst Biol. 2008 Jun;57(3):406-19. doi: 10.1080/10635150802166046.


Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms.

Brandley MC, Huelsenbeck JP, Wiens JJ.

Evolution. 2008 Aug;62(8):2042-64. doi: 10.1111/j.1558-5646.2008.00430.x. Epub 2008 May 27.


Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics.

Lakner C, van der Mark P, Huelsenbeck JP, Larget B, Ronquist F.

Syst Biol. 2008 Feb;57(1):86-103. doi: 10.1080/10635150801886156.


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