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bioRxiv · 10.1101/2021.03.10.434297

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

Pockrandt, C.·Steinegger, M.·Salzberg, S.
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Abstract

SummaryPhyloCSF++ 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. AvailabilityPhyloCSF++ 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/. Contactpockrandt@jhu.edu, martin.steinegger@snu.ac.kr

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Pockrandt, C., Steinegger, M., Salzberg, S.. 2021-03-11. PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools. https://doi.org/10.1101/2021.03.10.434297

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