'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Mar 2020
Mar 2020
Historique:
received:
30
04
2019
revised:
31
07
2019
accepted:
13
10
2019
entrez:
12
2
2021
pubmed:
30
10
2019
medline:
30
10
2019
Statut:
epublish
Résumé
Word-based or 'alignment-free' methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free methods calculate 'pairwise' distances between nucleic-acid or protein sequences; these distance values can then be used as input for tree-reconstruction programs such as neighbor-joining. In this paper, we propose the first word-based phylogeny approach that is based on 'multiple' sequence comparison and 'maximum likelihood'. Our algorithm first samples small, gap-free alignments involving four taxa each. For each of these alignments, it then calculates a quartet tree and, finally, the program 'Quartet MaxCut' is used to infer a super tree for the full set of input taxa from the calculated quartet trees. Experimental results show that trees produced with our approach are of high quality.
Identifiants
pubmed: 33575565
doi: 10.1093/nargab/lqz013
pii: lqz013
pmc: PMC7671388
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqz013Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
Références
PLoS Comput Biol. 2016 Oct 19;12(10):e1005107
pubmed: 27760124
J Comput Biol. 2013 Feb;20(2):64-79
pubmed: 23383994
Bioinformatics. 2011 Sep 1;27(17):2433-4
pubmed: 21690104
PLoS One. 2020 Feb 10;15(2):e0228070
pubmed: 32040534
Mol Biol Evol. 2012 Apr;29(4):1115-23
pubmed: 22160766
Algorithms Mol Biol. 2015 Feb 11;10:5
pubmed: 25685176
Sci Rep. 2013;3:2634
pubmed: 24022334
Sci Rep. 2016 Jul 01;6:28970
pubmed: 27363362
Brief Bioinform. 2014 May;15(3):343-53
pubmed: 24064230
Bioinformatics. 2011 Feb 1;27(3):334-42
pubmed: 21148543
Biosystems. 1992;28(1-3):47-55
pubmed: 1292666
Nucleic Acids Res. 2013 Apr;41(7):e75
pubmed: 23335788
Algorithms Mol Biol. 2017 Feb 14;12:1
pubmed: 28289437
BMC Bioinformatics. 2014;15 Suppl 9:S1
pubmed: 25252700
BMC Bioinformatics. 2019 Dec 17;20(Suppl 20):638
pubmed: 31842735
Genome Biol. 2017 Oct 3;18(1):186
pubmed: 28974235
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W7-11
pubmed: 24829447
BMC Res Notes. 2012 Feb 28;5:123
pubmed: 22373455
Gigascience. 2019 Mar 1;8(3):
pubmed: 30535314
Bioinformatics. 2017 Apr 1;33(7):971-979
pubmed: 28073754
Mol Syst Biol. 2011 Oct 11;7:539
pubmed: 21988835
J Mol Evol. 1981;17(6):368-76
pubmed: 7288891
Bioinformatics. 2014 Jul 15;30(14):2000-8
pubmed: 24828656
Algorithms Mol Biol. 2017 Dec 11;12:27
pubmed: 29238399
Front Plant Sci. 2012 Aug 29;3:192
pubmed: 22952468
Bioinformatics. 2015 Apr 15;31(8):1169-75
pubmed: 25504847
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Bioinformatics. 2014 Jul 15;30(14):2079-80
pubmed: 24651968
Annu Rev Biomed Data Sci. 2018 Jul;1:93-114
pubmed: 31828235
J Mol Evol. 2018 Feb;86(2):150-165
pubmed: 29460038
Pac Symp Biocomput. 2002;:115-26
pubmed: 11928468
Mol Biol Evol. 1997 Jul;14(7):685-95
pubmed: 9254330
Brief Bioinform. 2019 Mar 22;20(2):426-435
pubmed: 28673025
Mol Biol Evol. 1987 Jul;4(4):406-25
pubmed: 3447015
Brief Bioinform. 2014 May;15(3):407-18
pubmed: 24291823
PLoS Comput Biol. 2016 Jun 23;12(6):e1004985
pubmed: 27336403
BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):238
pubmed: 28617225
Mol Phylogenet Evol. 2012 Jan;62(1):1-8
pubmed: 21762785
BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):441
pubmed: 30497364
J Comput Biol. 2006 Mar;13(2):336-50
pubmed: 16597244
IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):704-18
pubmed: 21030737
PLoS One. 2013;8(2):e56925
pubmed: 23451112
Genome Biol. 2019 Feb 13;20(1):34
pubmed: 30760303
J Comput Biol. 2016 Jun;23(6):472-82
pubmed: 27058840
Bioinformatics. 2019 Oct 1;35(19):3547-3552
pubmed: 30994912
Genome Biol. 2016 Jun 20;17(1):132
pubmed: 27323842
Genome Biol. 2019 Jul 25;20(1):144
pubmed: 31345254
J Comput Biol. 2009 Oct;16(10):1487-500
pubmed: 19803738
Bioinformatics. 2014 Jul 15;30(14):1991-9
pubmed: 24700317
Nat Microbiol. 2016 Dec 22;2:16241
pubmed: 28005061