ProCARs

ProCARs reconstructs ancestral gene orders by iteratively detecting and assembling CARs using a homology-based approach.

Key Features:

• Homology-based methodology: Identifies sets of potential ancestral adjacencies iteratively rather than minimizing total rearrangement distances across species trees.
• Progressive detection and assembly: Iteratively refines the set of CARs at each step to enhance reconstruction accuracy.
• Two-phase assembly: Initially detects potential ancestral adjacencies based on current CAR configurations, then progressively assembles these into comprehensive CAR structures.
• Micro-rearrangement tolerance: Allows minor micro-rearrangements of synteny blocks at the extremities of assembled CARs.
• Phylogeny input: Operates on a phylogeny tree annotated with an ancestor and does not require branch lengths.
• Implementation: Implemented in Python.

Scientific Applications:

• Ancestral genome reconstruction: Reconstructs ancestral genomes and ancestral gene orders to study evolutionary genomic changes.
• Boreoeutherian reconstruction: Applied to reconstruct the boreoeutherian ancestral gene order to inform mammalian genome evolution.
• Comparative method evaluation: Facilitates comparative analyses with homology-based methods such as AnGeS, InferCARs, and GapAdj.

Methodology:

Iterative detection and assembly starting from an initial set of CARs with a two-phase assembling method (detect potential ancestral adjacencies based on current CAR configurations, then progressively assemble CARs), allowing minor micro-rearrangements at CAR extremities, operating on a phylogeny tree annotated with an ancestor without branch lengths; implemented in Python.