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

Christopher Pockrandt; Martin Steinegger; Steven L Salzberg

doi:10.1093/bioinformatics/btab756

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

Bioinformatics. 2022 Feb 7;38(5):1440-1442. doi: 10.1093/bioinformatics/btab756.

Authors

Christopher Pockrandt^{1

2}, Martin Steinegger³, Steven L Salzberg^{1

2

4

5}

Affiliations

¹ Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.
² Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
³ School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
⁴ Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA.
⁵ Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA.

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/.

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

Authors

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Abstract

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