Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 31

1.

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

Redelings BD, Holder MT.

PeerJ. 2017 Mar 1;5:e3058. doi: 10.7717/peerj.3058. eCollection 2017.

2.

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

McTavish EJ, Steel M, Holder MT.

Mol Phylogenet Evol. 2015 Dec;93:289-95. doi: 10.1016/j.ympev.2015.07.027. Epub 2015 Aug 6.

PMID:
26256643
3.

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

McTavish EJ, Hinchliff CE, Allman JF, Brown JW, Cranston KA, Holder MT, Rees JA, Smith SA.

Bioinformatics. 2015 Sep 1;31(17):2794-800. doi: 10.1093/bioinformatics/btv276. Epub 2015 May 4.

4.

Phycas: software for Bayesian phylogenetic analysis.

Lewis PO, Holder MT, Swofford DL.

Syst Biol. 2015 May;64(3):525-31. doi: 10.1093/sysbio/syu132. Epub 2015 Jan 9.

PMID:
25577605
5.

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

Oaks JR, Sukumaran J, Esselstyn JA, Linkem CW, Siler CD, Holder MT, Brown RM.

Evolution. 2013 Apr;67(4):991-1010. doi: 10.1111/j.1558-5646.2012.01840.x. Epub 2012 Dec 11.

PMID:
23550751
6.

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

Koch JM, Holder MT.

Version 2. PLoS Curr. 2012 Dec 14 [revised 2012 Jan 1];4:e4fd1286980c08. doi: 10.1371/4fd1286980c08.

7.

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

Peterson AT, Holder MT.

Ecol Evol. 2012 Aug;2(8):1826-33. doi: 10.1002/ece3.297. Epub 2012 Jul 1.

8.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

9.

NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, Midford PE, Priyam A, Sukumaran J, Xia X, Stoltzfus A.

Syst Biol. 2012 Jul;61(4):675-89. doi: 10.1093/sysbio/sys025. Epub 2012 Feb 22.

10.

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

Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR.

Syst Biol. 2012 Jan;61(1):90-106. doi: 10.1093/sysbio/syr095. Epub 2011 Dec 1.

PMID:
22139466
11.

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.

12.

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.

13.

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

Holder MT, Steel M.

J Theor Biol. 2011 Jul 7;280(1):159-66. doi: 10.1016/j.jtbi.2011.04.005. Epub 2011 Apr 17.

PMID:
21540039
14.

Ginkgo: spatially-explicit simulator of complex phylogeographic histories.

Sukumaran J, Holder MT.

Mol Ecol Resour. 2011 Mar;11(2):364-9. doi: 10.1111/j.1755-0998.2010.02926.x. Epub 2010 Nov 10.

PMID:
21429145
15.

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

Lakner C, Holder MT, Goldman N, Naylor GJ.

Syst Biol. 2011 Mar;60(2):161-74. doi: 10.1093/sysbio/syq088. Epub 2011 Jan 12.

PMID:
21233085
16.

The phylogenetic position of Myxozoa: exploring conflicting signals in phylogenomic and ribosomal data sets.

Evans NM, Holder MT, Barbeitos MS, Okamura B, Cartwright P.

Mol Biol Evol. 2010 Dec;27(12):2733-46. doi: 10.1093/molbev/msq159. Epub 2010 Jun 24.

PMID:
20576761
17.

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

Holder MT, Lewis PO, Swofford DL.

Syst Biol. 2010 Jul;59(4):477-85. doi: 10.1093/sysbio/syq028. Epub 2010 May 31. No abstract available.

PMID:
20547783
18.

DendroPy: a Python library for phylogenetic computing.

Sukumaran J, Holder MT.

Bioinformatics. 2010 Jun 15;26(12):1569-71. doi: 10.1093/bioinformatics/btq228. Epub 2010 Apr 25.

PMID:
20421198
19.

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

Allman ES, Holder MT, Rhodes JA.

J Theor Biol. 2010 Mar 7;263(1):108-19. doi: 10.1016/j.jtbi.2009.12.001. Epub 2009 Dec 11.

PMID:
20004210
20.

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

Holder MT, Sukumaran J, Lewis PO.

Syst Biol. 2008 Oct;57(5):814-21. doi: 10.1080/10635150802422308. No abstract available.

PMID:
18853367
21.

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

Holder MT, Zwickl DJ, Dessimoz C.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4013-21. doi: 10.1098/rstb.2008.0162.

22.

Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics.

Holder MT, Lewis PO, Swofford DL, Larget B.

Syst Biol. 2005 Dec;54(6):961-5. No abstract available.

PMID:
16385776
23.

Polytomies and Bayesian phylogenetic inference.

Lewis PO, Holder MT, Holsinger KE.

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

PMID:
16012095
24.

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

Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO, Hillis DM.

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

PMID:
12270898
25.

Difficulties in detecting hybridization.

Holder MT, Anderson JA, Holloway AK.

Syst Biol. 2001 Nov-Dec;50(6):978-82. No abstract available.

PMID:
12116644
26.

Two living species of coelacanths?

Holder MT, Erdmann MV, Wilcox TP, Caldwell RL, Hillis DM.

Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12616-20.

27.

Caprine microsatellite dinucleotide repeat polymorphisms at the SR-CRSP21, SR-CRSP22, SR-CRSP23, SR-CRSP24, SR-CRSP25, SR-CRSP26 and SR-CRSP27 loci.

Yeh CC, Kogi JK, Holder MT, Guerra TM, Davis SK, Taylor JF.

Anim Genet. 1997 Oct;28(5):380-1. No abstract available.

PMID:
9363617
28.

Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN16, TEXAN17, TEXAN18, TEXAN19 and TEXAN20 loci.

Burns BM, Taylor JF, Herring KL, Herring AD, Holder MT, Holder DA, Collins JS, Sanders JO, Davis SK.

Anim Genet. 1995 Jun;26(3):208-9. No abstract available.

PMID:
7793700
29.

Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN11, TEXAN12, TEXAN13, TEXAN14 and TEXAN15 loci.

Burns BM, Taylor JF, Herring KL, Herring AD, Holder MT, Collins JS, Guerra TM, Sanders JO, Davis SK.

Anim Genet. 1995 Jun;26(3):201-2. No abstract available.

PMID:
7793692
30.

Bovine microsatellite mononucleotide and dinucleotide repeat polymorphisms at the TEXAN6, TEXAN7, TEXAN8, TEXAN9 and TEXAN10 loci.

Burns BM, Taylor JF, Herring KL, Herring AD, Holder MT, Collins JS, Guerra TM, Sanders JO, Davis SK.

Anim Genet. 1995 Apr;26(2):128-9. No abstract available.

PMID:
7733502
31.

Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN-1, TEXAN-2, TEXAN-3, TEXAN-4 and TEXAN-5 loci.

Holder DA, Arevalo E, Holder MT, Taylor JF, Davis SK.

Anim Genet. 1994 Jun;25(3):201. No abstract available.

PMID:
7943968

Supplemental Content

Loading ...
Support Center