eprintid: 2355
rev_number: 5
eprint_status: archive
userid: 282
dir: disk0/00/00/23/55
datestamp: 2016-12-29 08:22:47
lastmod: 2016-12-29 08:22:47
status_changed: 2016-12-29 08:22:47
type: conference_item
metadata_visibility: show
creators_name: Hoang, Thi Diep
creators_name: Vinh, Le Sy
creators_name: Flouri, Tomas
creators_name: Stamatakis, Alexandros
creators_name: von Haeseler, Arndt
creators_name: Minh, Bui Quang
creators_id: diepht@vnu.edu.vn
title: A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation
ispublished: pub
subjects: IT
divisions: fac_fit
abstract: Reconstructing maximum parsimony (MP) trees along with bootstrap for large multiple sequence alignments is a computationally challenging task. In this paper, we present MPBoot, a new method for approximating MP bootstrap based on the idea of a previously introduced method for maximum likelihood bootstrap. MPBoot economizes the computations by only sampling trees on the original alignment and simultaneously calculating exact parsimony scores for all bootstrap alignments. Preliminary experiments on simulated data showed that MPBoot is about 2-3.5 times faster and yields better parsimony scores than a fast bootstrap procedure implemented in TNT. MPBoot also produced less biased support value than TNT for small simulated data sets (<;= 200 sequences). However, for large number of sequences (>=500) MPBoot overestimates the probability that a clade is true, i.e., results in likely high false positive rates. As MPBoot is currently a proof-of-concept implementation, more work is to understand the limitations of the method.
date: 2016
date_type: published
official_url: http://doi.org/10.1109/KSE.2016.7758020
id_number: doi:10.1109/KSE.2016.7758020
full_text_status: none
pres_type: paper
pagerange: 1-6
event_title: 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE)
event_type: conference
refereed: FALSE
book_title: 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE)
citation:   Hoang, Thi Diep and Vinh, Le Sy and Flouri, Tomas and Stamatakis, Alexandros and von Haeseler, Arndt and Minh, Bui Quang  (2016) A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation.  In: 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE).