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Mark T. Holder
Mark T. Holder
Associate Professor of Ecology and Evolutionary Biology, University of Kansas
Verified email at ku.edu - Homepage
Title
Cited by
Year
DendroPy 5: a mature Python library for phylogenetic computing
MA Moreno, J Sukumaran, MT Holder
arXiv preprint arXiv:2405.14120, 2024
2024
Speeding up iterative applications of the BUILD supertree algorithm
BD Redelings, MT Holder
PeerJ 12, e16624, 2024
2024
A complete and dynamic tree of birds
EJ McTavish, JA Gerbracht, MT Holder, MJ Iliff, D Lepage, PC Rasmussen, ...
bioRxiv, 2024.05. 20.595017, 2024
12024
Package ‘rncl’
F Michonneau, B Bolker, M Holder, P Lewis, B O'Meara
32023
OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life
EJ McTavish, LL Sánchez-Reyes, MT Holder
Systematic Biology 70 (6), 1295-1301, 2021
82021
Incorporating the speciation process into species delimitation
J Sukumaran, MT Holder, LL Knowles
PLoS Computational Biology 17 (5), e1008924, 2021
762021
Genome‐wide genotyping estimates mating system parameters and paternity in the island species Tolpis succulenta
MJS Gibson, DJ Crawford, MT Holder, ME Mort, B Kerbs, MM de Sequeira, ...
American Journal of Botany 107 (8), 1189-1197, 2020
62020
Copulas and their potential for ecology
S Ghosh, LW Sheppard, MT Holder, TD Loecke, PC Reid, JD Bever, ...
Advances in Ecological Research 62, 409-468, 2020
312020
Taxonomic Supertree Construction with Incertae sedis Taxa
BD Redelings, MT Holder
Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret …, 2019
12019
A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species
BD Redelings, MT Holder
PeerJ 5, e3058, 2017
522017
Phylogenetic tree comparison
MT Holder, EJ McTavish
Academic Press, 2016
32016
Twisted trees and inconsistency of tree estimation when gaps are treated as missing data–The impact of model mis-specification in distance corrections
EJ McTavish, M Steel, MT Holder
Molecular phylogenetics and evolution 93, 289-295, 2015
122015
Phylesystem: a git-based data store for community-curated phylogenetic estimates
EJ McTavish, CE Hinchliff, JF Allman, JW Brown, KA Cranston, MT Holder, ...
Bioinformatics 31 (17), 2794-2800, 2015
382015
Phycas: software for Bayesian phylogenetic analysis
PO Lewis, MT Holder, DL Swofford
Systematic Biology 64 (3), 525-531, 2015
402015
SumTrees: phylogenetic tree summarization. 4.0. 0
J Sukumaran, MT Holder
Progr. Doc. available from authors, 2015
552015
Variable tree topology stepping-stone marginal likelihood estimation
MT Holder, PO Lewis, DL Swofford, D Bryant
Bayesian phylogenetics: methods, algorithms, and applications 1, 95-111, 2014
14*2014
phylobase: Base package for phylogenetic structures and comparative data
R Hackathon, B Bolker, M Butler, P Cowan, D De Vienne, D Eddelbuettel, ...
R package version 0.6 5, 2013
602013
Evidence for Climate‐driven Diversification? A Caution For Interpreting ABC Inferences of Simultaneous Historical Events
JR Oaks, J Sukumaran, JA Esselstyn, CW Linkem, CD Siler, MT Holder, ...
Evolution 67 (4), 991-1010, 2013
792013
An algorithm for calculating the probability of classes of data patterns on a genealogy
JM Koch, MT Holder
Plos Currents 4, 2012
82012
Phylogenetic assessment of filoviruses: how many lineages of M arburg virus?
AT Peterson, MT Holder
Ecology and Evolution 2 (8), 1826-1833, 2012
242012
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Articles 1–20