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

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. 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 multiple sequence alignments on the fly with MMseqs2. AVAILABILITY 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/.