@inproceedings{0d5d436f0c1240049ae725ac6e3d364f,
title = "A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation",
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.",
keywords = "maximum parsimony, nonparametric bootstrap, phylogenetic inference",
author = "Hoang, {Diep Thi} and Vinh, {Le Sy} and Tomas Flouri and Alexandros Stamatakis and {Von Haeseler}, Arndt and Minh, {Bui Quang}",
note = "Publisher Copyright: {\textcopyright} 2016 IEEE.; 8th International Conference on Knowledge and Systems Engineering, KSE 2016 ; Conference date: 06-10-2016 Through 08-10-2016",
year = "2016",
month = nov,
day = "28",
doi = "10.1109/KSE.2016.7758020",
language = "English",
series = "Proceedings - 2016 8th International Conference on Knowledge and Systems Engineering, KSE 2016",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "1--6",
editor = "Nguyen, {Minh Le} and Vinh, {Le Sy} and Bui, {Lam Thu} and Van-Giang Nguyen and Yew-Soon Ong and Yew-Soon Ong and Keiji Hirata",
booktitle = "Proceedings - 2016 8th International Conference on Knowledge and Systems Engineering, KSE 2016",
address = "United States",
}