Treehouse: a user-friendly application to obtain subtrees from large phylogenies.
Big data
Graphical user interface
Phylogenetics
Phylogenomics
Shiny
Tree
Tree pruning
Journal
BMC research notes
ISSN: 1756-0500
Titre abrégé: BMC Res Notes
Pays: England
ID NLM: 101462768
Informations de publication
Date de publication:
27 Aug 2019
27 Aug 2019
Historique:
received:
23
05
2019
accepted:
21
08
2019
entrez:
29
8
2019
pubmed:
29
8
2019
medline:
6
2
2020
Statut:
epublish
Résumé
Phylogenetic trees that contain hundreds to thousands of taxa are now routinely generated. Retrieving the relationships among a subset of taxa in these large phylogenies can be a challenging or time-consuming task. Addressing this challenge requires the development of tools that facilitate the easy retrieval of subtrees from any user-specified set of taxa in a given phylogeny. We developed treehouse, an open source tool that enables the retrieval of any subtree from a given large phylogeny. With a three-step workflow, treehouse successfully allows a user to obtain a subtree from any phylogeny. Treehouse can help researchers to explore the relationships among any set of taxa from across the tree of life. Treehouse is implemented as a shiny application in the R programming language. Treehouse software and usage instructions are publicly available at https://github.com/JLSteenwyk/treehouse .
Identifiants
pubmed: 31455362
doi: 10.1186/s13104-019-4577-5
pii: 10.1186/s13104-019-4577-5
pmc: PMC6712805
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
541Subventions
Organisme : National Science Foundation
ID : DEB1442113
Références
Bioinformatics. 2004 Jan 22;20(2):289-90
pubmed: 14734327
Nature. 2006 Oct 19;443(7113):818-22
pubmed: 17051209
Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):14942-7
pubmed: 22930817
Syst Biol. 2014 Nov;63(6):919-32
pubmed: 25077515
Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68
pubmed: 25355905
Science. 2014 Nov 7;346(6210):763-7
pubmed: 25378627
Science. 2014 Dec 12;346(6215):1320-31
pubmed: 25504713
Mol Biol Evol. 2015 Aug;32(8):2001-14
pubmed: 25837578
Proc Natl Acad Sci U S A. 2015 May 5;112(18):5773-8
pubmed: 25902535
Curr Biol. 2015 Aug 3;25(15):1993-9
pubmed: 26212885
Syst Biol. 2015 Nov;64(6):1104-20
pubmed: 26276158
Nature. 2015 Oct 22;526(7574):569-73
pubmed: 26444237
BMC Genomics. 2015 Nov 23;16:987
pubmed: 26596625
Genome Biol Evol. 2016 Jan 05;8(2):330-44
pubmed: 26733575
Nat Microbiol. 2016 Apr 11;1:16048
pubmed: 27572647
G3 (Bethesda). 2016 Dec 7;6(12):3927-3939
pubmed: 27672114
Genome Res. 2017 Jul;27(7):1207-1219
pubmed: 28611159
Nature. 2018 Apr;556(7701):339-344
pubmed: 29643504
Cell. 2018 Nov 29;175(6):1533-1545.e20
pubmed: 30415838
Nat Ecol Evol. 2019 Apr;3(4):668-678
pubmed: 30886374
MBio. 2019 Jul 9;10(4):null
pubmed: 31289177