eprintid: 4215
rev_number: 7
eprint_status: archive
userid: 282
dir: disk0/00/00/42/15
datestamp: 2020-12-10 02:37:36
lastmod: 2020-12-10 02:37:36
status_changed: 2020-12-10 02:37:36
type: conference_item
metadata_visibility: show
creators_name: Nguyen, Duc Canh
creators_name: Dang, Cao Cuong
creators_name: Le, Sy Vinh
creators_name: Bui, Quang Minh
creators_name: Hoang, Thi Diep
creators_id: duccanh9511@gmail.com
creators_id: vinhls@vnu.edu.vn
creators_id: m.bui@anu.edu.au
creators_id: diepht@vnu.edu.vn
title: pQMaker: empirically estimating amino acid substitution models in a parallel environment
ispublished: pub
subjects: IT
divisions: fac_fit
abstract: Amino acid substitution matrices are central to the model-based methods for reconstructing evolutionary trees from amino acid sequences. QMaker is an efficient method for estimating general time-reversible amino acid substitution matrices from a large biological dataset containing thousands of protein alignments using maximum likelihood principle. It allows researchers to build an amino acid substitution model on their own to best fit their subsequent phylogenetic analyses. In this work, we propose an approach to parallelize computation in QMaker, named pQMaker. Moreover, we provide an open-source message passing interface implementation for pQMaker (https://github.com/canhnd58/IQ-TREE/tree/pqmaker) built upon the latest IQ-TREE package. Experiments on benchmark data sets show that our implementation has significant speed gains compared with the original QMaker.
date: 2020-11-14
date_type: published
contact_email: diepht@vnu.edu.vn
full_text_status: none
pres_type: paper
pagerange: 324-329
event_title: 2020 12th International Conference on Knowledge and Systems Engineering (KSE)
event_location: Can Tho Viet Nam
event_dates: November 12-14, 2020
event_type: conference
refereed: FALSE
funders: Nafosted
projects: 102.01.2019.06
citation:   Nguyen, Duc Canh and Dang, Cao Cuong and Le, Sy Vinh and Bui, Quang Minh and Hoang, Thi Diep  (2020) pQMaker: empirically estimating amino acid substitution models in a parallel environment.  In: 2020 12th International Conference on Knowledge and Systems Engineering (KSE), November 12-14, 2020, Can Tho Viet Nam.