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Title: PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools
Abstract Summary

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.

Availability and implementation

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/.

 
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NSF-PAR ID:
10362614
Author(s) / Creator(s):
; ; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
Bioinformatics
Volume:
38
Issue:
5
ISSN:
1367-4803
Format(s):
Medium: X Size: p. 1440-1442
Size(s):
p. 1440-1442
Sponsoring Org:
National Science Foundation
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