PhyloCSF 20121028 / PhyloCSF++ v1.1.0
PhyloCSF is a method to determine whether a multi-species nucleotide sequence alignment is likely to represent a protein-coding region. PhyloCSF does not rely on homology to known protein sequences; instead, it examines evolutionary signatures characteristic to alignments of conserved coding regions, such as the high frequencies of synonymous codon substitutions and conservative amino acid substitutions, and the low frequencies of other missense and non-sense substitutions (CSF = Codon Substitution Frequencies).
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.
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Pockrandt C, Steinegger M, Salzberg SL.
PhyloCSF ++: A fast and user-friendly implementation of PhyloCSF with annotation tools.
Bioinformatics. 2021 Nov 4:btab756. doi: 10.1093/bioinformatics/btab756. Epub ahead of print. PMID: 34734986.
Lin MF, Jungreis I, and Kellis M (2011).
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions.
Bioinformatics (2011) 27 (13): i275-i282.