RASCL

RASCL performs rapid, phylogenetics-based comparative analyses of natural selection within clades using molecular sequence data, with emphasis on SARS-CoV-2 lineages.

Key Features:

• Continuous comparative phylogenetics-based analysis: Performs continuous comparative, phylogenetics-based analyses on clade-focused genome surveillance datasets.
• Automated down-sampling and alignment: Automatically generates down-sampled codon alignments for individual genes and open reading frames (ORFs) including contextualizing background reference sequences.
• Selection tests battery: Applies a variety of selection tests to the generated alignments to detect and quantify natural selection across lineages.
• Output formats: Produces machine-readable JSON outputs and interactive notebook-based visualizations.

Scientific Applications:

• Genomic surveillance and evolutionary studies: Identifies signals of natural selection within viral clades to support genomic surveillance and evolutionary analyses of SARS-CoV-2 and other viruses.
• Variant emergence and spread assessment: Assesses selection pressures that contribute to the emergence and proliferation of viral lineages and variants.
• Public health and epidemiology: Provides selection-based evidence to inform public-health responses and genomic surveillance strategies.

Methodology:

Continuously monitors genome-surveillance datasets focused on specified clades/lineages, generates down-sampled codon alignments per gene/ORF with background reference sequences, conducts phylogenetics-based comparative selection analyses using a battery of selection tests, and outputs results as JSON and interactive notebook visualizations.