How to build phylogenetic species trees with OMA.
OMA
Orthologous Matrix
phylogenetics
phylogenomics
species tree
Journal
F1000Research
ISSN: 2046-1402
Titre abrégé: F1000Res
Pays: England
ID NLM: 101594320
Informations de publication
Date de publication:
2020
2020
Historique:
accepted:
11
02
2022
entrez:
21
6
2022
pubmed:
4
6
2020
medline:
4
6
2020
Statut:
epublish
Résumé
Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done
Identifiants
pubmed: 35722083
doi: 10.12688/f1000research.23790.2
pmc: PMC9194518
doi:
Banques de données
figshare
['10.6084/m9.figshare.10780820.v6']
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
511Informations de copyright
Copyright: © 2022 Dylus D et al.
Déclaration de conflit d'intérêts
No competing interests were disclosed.
Références
Curr Biol. 2019 Jun 3;29(11):1818-1826.e6
pubmed: 31104936
BMC Bioinformatics. 2008 Dec 04;9:518
pubmed: 19055798
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Nat Methods. 2016 May;13(5):425-30
pubmed: 27043882
Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4602-E4611
pubmed: 28533395
PLoS Biol. 2011 Mar;9(3):e1000602
pubmed: 21423652
Bioinformatics. 2015 Oct 1;31(19):3210-2
pubmed: 26059717
Nat Ecol Evol. 2018 Nov;2(11):1761-1771
pubmed: 30297745
Nat Rev Genet. 2012 Mar 28;13(5):303-14
pubmed: 22456349
Mol Phylogenet Evol. 2018 Oct;127:907-918
pubmed: 29966686
Proc Natl Acad Sci U S A. 2015 Oct 13;112(41):12764-9
pubmed: 26385966
Methods Mol Biol. 2019;1910:149-175
pubmed: 31278664
F1000Res. 2020 Jan 17;9:27
pubmed: 32089838
PeerJ. 2017 Jan 31;5:e2951
pubmed: 28168115
Methods Mol Biol. 2018;1704:103-187
pubmed: 29277865
Nucleic Acids Res. 2021 Jan 8;49(D1):D373-D379
pubmed: 33174605
Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485
pubmed: 29106550
Mol Biol Evol. 2016 Aug;33(8):2163-6
pubmed: 27189561
Syst Zool. 1970 Jun;19(2):99-113
pubmed: 5449325
Genome Res. 2019 Jul;29(7):1152-1163
pubmed: 31235654
Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955-9
pubmed: 2413450
Nat Microbiol. 2016 Apr 11;1:16048
pubmed: 27572647
Evolution. 1985 Jul;39(4):783-791
pubmed: 28561359
Nat Commun. 2019 Dec 2;10(1):5477
pubmed: 31792218
J Exp Zool B Mol Dev Evol. 2005 Jan 15;304(1):64-74
pubmed: 15593277