Author: Pockrandt, Christopher; Steinegger, Martin; Salzberg, Steven L.
Title: PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools Cord-id: ckrhnkru Document date: 2021_10_22
ID: ckrhnkru
Snippet: 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 rel
Document: 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/. Contact [email protected], [email protected]
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