PhyloCSF++

PhyloCSF++ distinguishes protein-coding regions from non-coding regions in genomes by applying PhyloCSF statistical models to multiple sequence alignments using a parallel C++ implementation for large-scale analyses.

Key Features:

• Efficient Identification: Analyzes multiple sequence alignments to discriminate protein-coding regions from non-coding regions.
• Parallelized Implementation: Implemented in C++ with parallel processing to accelerate analysis of large genomic datasets.
• Scoring Alignments and Browser Tracks: Scores local alignments and generates genome-wide browser tracks in the wig file format.
• Annotation Capabilities: Annotates coding sequences in GFF/GTF files using precomputed tracks and can compute and score multiple sequence alignments on-the-fly with MMseqs2.

Scientific Applications:

• Genome Annotation: Provides coding-potential evidence for annotating genes and CDS features in GFF/GTF files.
• Comparative Genomics: Scores alignments across multiple species to assess evolutionary conservation and coding potential.
• Functional Genomics: Evaluates coding potential to aid discovery of novel genes and investigation of gene function.

Methodology:

Implements PhyloCSF and PhyloCSF HMM statistical models on multiple sequence alignments in a parallel C++ implementation, supports scoring of local alignments and generation of wig tracks, annotates GFF/GTF using precomputed tracks, and can compute and score MSAs on-the-fly with MMseqs2.