Mark T Holder

Mark T Holder

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Mark T Holder

Mark T Holder

Publications by authors named "Mark T Holder"

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A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species.

PeerJ 2017 1;5:e3058. Epub 2017 Mar 1.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States; Biodiversity Institute, University of Kansas, Lawrence, KS, United States; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.

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https://peerj.com/articles/3058
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http://dx.doi.org/10.7717/peerj.3058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335690PMC
March 2017

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections.

Mol Phylogenet Evol 2015 Dec 6;93:289-95. Epub 2015 Aug 6.

Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.

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http://dx.doi.org/10.1016/j.ympev.2015.07.027DOI Listing
December 2015

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

Bioinformatics 2015 Sep 4;31(17):2794-800. Epub 2015 May 4.

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.

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http://dx.doi.org/10.1093/bioinformatics/btv276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547614PMC
September 2015

Phycas: software for Bayesian phylogenetic analysis.

Syst Biol 2015 May 9;64(3):525-31. Epub 2015 Jan 9.

Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269, USA; Department of Ecology and Evolution, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA; and Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA.

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http://dx.doi.org/10.1093/sysbio/syu132DOI Listing
May 2015

Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events.

Evolution 2013 Apr 11;67(4):991-1010. Epub 2012 Dec 11.

Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.

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http://dx.doi.org/10.1111/j.1558-5646.2012.01840.xDOI Listing
April 2013

An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy.

PLoS Curr 2012 12 14;4:e4fd1286980c08. Epub 2012 Dec 14.

Department of Ecology and Evolutionary Biology, University of Kansas.

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http://dx.doi.org/10.1371/4fd1286980c08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3712476PMC
December 2012

Phylogenetic assessment of filoviruses: how many lineages of Marburg virus?

Ecol Evol 2012 Aug 1;2(8):1826-33. Epub 2012 Jul 1.

Department of Ecology and Evolutionary Biology, The University of Kansas Lawrence, Kansas, 66045.

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http://dx.doi.org/10.1002/ece3.297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3433987PMC
August 2012

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

Mol Biol Evol 2012 Mar 2;29(3):939-55. Epub 2011 Nov 2.

Department of Ecology and Evolutionary Biology, University of Kansas, KS, USA.

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http://dx.doi.org/10.1093/molbev/msr255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350323PMC
March 2012

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Syst Biol 2012 Jan 1;61(1):90-106. Epub 2011 Dec 1.

Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA.

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http://dx.doi.org/10.1093/sysbio/syr095DOI Listing
January 2012

Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts.

J Theor Biol 2011 Jul 17;280(1):159-66. Epub 2011 Apr 17.

Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66045, United States.

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http://dx.doi.org/10.1016/j.jtbi.2011.04.005DOI Listing
July 2011

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.

Syst Biol 2011 Mar 12;60(2):161-74. Epub 2011 Jan 12.

Department of Biological Science, Section of Ecology and Evolution, Florida State University, Tallahassee, FL 32306-4120, USA.

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http://dx.doi.org/10.1093/sysbio/syq088DOI Listing
March 2011

Ginkgo: spatially-explicit simulator of complex phylogeographic histories.

Mol Ecol Resour 2011 Mar 10;11(2):364-9. Epub 2010 Nov 10.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.

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http://doi.wiley.com/10.1111/j.1755-0998.2010.02926.x
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http://dx.doi.org/10.1111/j.1755-0998.2010.02926.xDOI Listing
March 2011

The akaike information criterion will not choose the no common mechanism model.

Syst Biol 2010 Jul 31;59(4):477-85. Epub 2010 May 31.

Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.

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https://academic.oup.com/sysbio/article/59/4/477/1662415
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http://dx.doi.org/10.1093/sysbio/syq028DOI Listing
July 2010

DendroPy: a Python library for phylogenetic computing.

Bioinformatics 2010 Jun 25;26(12):1569-71. Epub 2010 Apr 25.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq228DOI Listing
June 2010

Estimating trees from filtered data: identifiability of models for morphological phylogenetics.

J Theor Biol 2010 Mar 11;263(1):108-19. Epub 2009 Dec 11.

Department of Mathematics and Statistics, University of Alaska Fairbanks, PO Box 756660, Fairbanks, AK 99775, USA.

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http://dx.doi.org/10.1016/j.jtbi.2009.12.001DOI Listing
March 2010

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.

Philos Trans R Soc Lond B Biol Sci 2008 Dec;363(1512):4013-21

Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.

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http://dx.doi.org/10.1098/rstb.2008.0162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607409PMC
December 2008

A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics.

Syst Biol 2008 Oct;57(5):814-21

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA.

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http://dx.doi.org/10.1080/10635150802422308DOI Listing
October 2008

Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics.

Syst Biol 2005 Dec;54(6):961-5

School of Computational Science, Florida State University, Tallahassee, 32306-4120, USA.

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http://dx.doi.org/10.1080/10635150500354670DOI Listing
December 2005

Polytomies and Bayesian phylogenetic inference.

Syst Biol 2005 Apr;54(2):241-53

Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043 (P.O.L.), Storrs, CN 06269-3043, USA.

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http://dx.doi.org/10.1080/10635150590924208DOI Listing
April 2005

Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference.

Mol Biol Evol 2002 Oct;19(10):1717-26

Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin 78712, USA.

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http://dx.doi.org/10.1093/oxfordjournals.molbev.a003994DOI Listing
October 2002