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Updated: Oct 14, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools
Christopher Pockrandt1,2, Martin Steinegger3, Steven L Salzberg1,2,4,5
1Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA.
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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