ROADIES

ROADIES automates phylogenetic tree inference from raw genome assemblies without requiring whole-genome alignment, a single reference species, or pre-selected loci such as functional genes from annotation steps.

Key Features:

• Reference-free operation: ROADIES eliminates reference bias by not requiring selection of a single reference species.
• Multi-copy gene support: ROADIES leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology.
• Accuracy-runtime tradeoff: ROADIES provides flexibility to adjust the tradeoff between accuracy and runtime.
• Scalability: ROADIES infers species trees comparable in quality with state-of-the-art approaches in a fraction of the time.

Scientific Applications:

• Species tree inference: ROADIES reconstructs evolutionary relationships across diverse life forms such as placental mammals, pomace flies, and birds.
• Phylogenomic analysis: ROADIES enables reproducible phylogenomic analyses from assembled genomes to species and gene trees.

Methodology:

ROADIES automates all computational steps from raw assembled genomes to species and gene trees; specific algorithmic details beyond elimination of whole-genome alignment, reference species selection, locus pre-selection, and orthology detection are not explicitly stated in the sources.