PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
07 02 2022
07 02 2022
Historique:
received:
12
03
2021
revised:
22
10
2021
accepted:
29
10
2021
pubmed:
5
11
2021
medline:
3
1
2023
entrez:
4
11
2021
Statut:
ppublish
Résumé
PhyloCSF++ is an efficient and parallelized C++ implementation of the popular PhyloCSF method to distinguish protein-coding and non-coding regions in a genome based on multiple sequence alignments (MSAs). It can score alignments or produce browser tracks for entire genomes in the wig file format. Additionally, PhyloCSF++ annotates coding sequences in GFF/GTF files using precomputed tracks or computes and scores MSAs on the fly with MMseqs2. PhyloCSF++ is released under the AGPLv3 license. Binaries and source code are available at https://github.com/cpockrandt/PhyloCSFpp. The software can be installed through bioconda. A variety of tracks can be accessed through ftp://ftp.ccb.jhu.edu/pub/software/phylocsfpp/.
Identifiants
pubmed: 34734986
pii: 6420698
doi: 10.1093/bioinformatics/btab756
pmc: PMC9991890
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1440-1442Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG006677
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM130151
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA180922
Pays : United States
Organisme : National Science Foundation
ID : IOS-1744309
Organisme : U.S. National Institutes of Health
Organisme : National Research Foundation of Korea
ID : 2019R1A6A1A1007347
Organisme : New Faculty Startup Fund
Organisme : Creative-Pioneering Researchers Program through Seoul National University
Informations de copyright
© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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