eprintid: 2955
rev_number: 10
eprint_status: archive
userid: 282
dir: disk0/00/00/29/55
datestamp: 2018-06-01 03:49:04
lastmod: 2018-06-01 03:49:04
status_changed: 2018-06-01 03:49:04
type: article
metadata_visibility: show
creators_name: Hoang, Thi Diep
creators_name: Le, Sy Vinh
creators_name: Flouri, Tomas
creators_name: Stamatakis, Alexandros
creators_name: von Haeseler, Arndt
creators_name: Bui, Quang Minh
creators_id: diepht@vnu.edu.vn
creators_id: vinhls@vnu.edu.vn
title: MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation
ispublished: pub
subjects: IT
subjects: Scopus
subjects: isi
divisions: fac_fit
abstract: BACKGROUND:
The 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.

RESULTS:
To 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.

CONCLUSIONS:
MPBoot 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 .
date: 2018-02-02
date_type: published
official_url: https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-018-1131-3
id_number: https://doi.org/10.1186/s12862-018-1131-3
full_text_status: none
publication: BMC Evolutionary Biology
volume: 18
refereed: TRUE
issn: 1471-2148
citation:   Hoang, Thi Diep and Le, Sy Vinh and Flouri, Tomas and Stamatakis, Alexandros and von Haeseler, Arndt and Bui, Quang Minh  (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.  BMC Evolutionary Biology, 18 .    ISSN 1471-2148