TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
15 09 2020
15 09 2020
Historique:
received:
20
01
2020
revised:
11
06
2020
accepted:
30
06
2020
pubmed:
9
7
2020
medline:
4
3
2021
entrez:
9
7
2020
Statut:
ppublish
Résumé
Microbial communities drive matter and energy transformations integral to global biogeochemical cycles, yet many taxonomic groups facilitating these processes remain poorly represented in biological sequence databases. Due to this missing information, taxonomic assignment of sequences from environmental genomes remains inaccurate. We present the Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software for functionally and taxonomically classifying genes, reactions and pathways from genomes of cultivated and uncultivated microorganisms using reference packages representing coding sequences mediating multiple globally relevant biogeochemical cycles. TreeSAPP uses linear regression of evolutionary distance on taxonomic rank to improve classifications, assigning both closely related and divergent query sequences at the appropriate taxonomic rank. TreeSAPP is able to provide quantitative functional and taxonomic classifications for both assembled and unassembled sequences and files supporting interactive tree of life visualizations. TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at https://github.com/hallamlab/TreeSAPP. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 32637989
pii: 5868555
doi: 10.1093/bioinformatics/btaa588
pmc: PMC7695126
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
4706-4713Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
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