<> "The repository administrator has not yet configured an RDF license."^^ . <> . . . "MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation"^^ . "BACKGROUND:\r\nThe nonparametric bootstrap is widely used to measure the branch support of phylogenetic trees. However, bootstrapping is computationally expensive and remains a bottleneck in phylogenetic analyses. Recently, an ultrafast bootstrap approximation (UFBoot) approach was proposed for maximum likelihood analyses. However, such an approach is still missing for maximum parsimony.\r\n\r\nRESULTS:\r\nTo close this gap we present MPBoot, an adaptation and extension of UFBoot to compute branch supports under the maximum parsimony principle. MPBoot works for both uniform and non-uniform cost matrices. Our analyses on biological DNA and protein showed that under uniform cost matrices, MPBoot runs on average 4.7 (DNA) to 7 times (protein data) (range: 1.2-20.7) faster than the standard parsimony bootstrap implemented in PAUP*; but 1.6 (DNA) to 4.1 times (protein data) slower than the standard bootstrap with a fast search routine in TNT (fast-TNT). However, for non-uniform cost matrices MPBoot is 5 (DNA) to 13 times (protein data) (range:0.3-63.9) faster than fast-TNT. We note that MPBoot achieves better scores more frequently than PAUP* and fast-TNT. However, this effect is less pronounced if an intensive but slower search in TNT is invoked. Moreover, experiments on large-scale simulated data show that while both PAUP* and TNT bootstrap estimates are too conservative, MPBoot bootstrap estimates appear more unbiased.\r\n\r\nCONCLUSIONS:\r\nMPBoot provides an efficient alternative to the standard maximum parsimony bootstrap procedure. It shows favorable performance in terms of run time, the capability of finding a maximum parsimony tree, and high bootstrap accuracy on simulated as well as empirical data sets. MPBoot is easy-to-use, open-source and available at http://www.cibiv.at/software/mpboot ."^^ . "2018-02-02" . "18" . . "BMC Evolutionary Biology"^^ . . . "14712148" . . . . . . . . . . . . . . . . . . . . . . "Alexandros"^^ . "Stamatakis"^^ . "Alexandros Stamatakis"^^ . . "Sy Vinh"^^ . "Le"^^ . "Sy Vinh Le"^^ . . "Quang Minh"^^ . "Bui"^^ . "Quang Minh Bui"^^ . . "Arndt"^^ . "von Haeseler"^^ . "Arndt von Haeseler"^^ . . "Tomas"^^ . "Flouri"^^ . "Tomas Flouri"^^ . . "Thi Diep"^^ . "Hoang"^^ . "Thi Diep Hoang"^^ . . . . . "HTML Summary of #2955 \n\nMPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation\n\n" . "text/html" . . . "Information Technology (IT)"@en . . . "Scopus-indexed journals"@en . . . "ISI-indexed journals"@en . .