TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.
Bioinformatics
Evolutionary biology
Genomics
Systems biology
Journal
STAR protocols
ISSN: 2666-1667
Titre abrégé: STAR Protoc
Pays: United States
ID NLM: 101769501
Informations de publication
Date de publication:
18 03 2022
18 03 2022
Historique:
entrez:
4
3
2022
pubmed:
5
3
2022
medline:
9
4
2022
Statut:
epublish
Résumé
Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).
Identifiants
pubmed: 35243369
doi: 10.1016/j.xpro.2022.101175
pii: S2666-1667(22)00055-7
pmc: PMC8857567
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
101175Informations de copyright
© 2022 The Author(s).
Déclaration de conflit d'intérêts
The authors declare no competing interests.
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