AllCoPol

AllCoPol reconstructs subgenome phylogenies of allopolyploid species by assigning alleles from multi-locus sequence datasets to diploid progenitor subgenomes using a heuristic Minimizing Deep Coalescences (MDC) approach.

Key Features:

• Heuristic Methodology: Employs a heuristic approach based on the Minimizing Deep Coalescences (MDC) criterion to assign alleles from polyploids to their corresponding diploid progenitor subgenomes in multi-locus sequence datasets.
• Consensus Approach: Implements a consensus approach to assess confidence in inferred allele partitions and resulting phylogenetic relationships.
• Simulation Capabilities: Simulates tetra- and hexaploids under assumptions of completely disomic inheritance and compares reconstructed phylogenies to MDC species trees based on true allele partitions, reporting comparable topological errors.

Scientific Applications:

• Polyploid evolution: Infers ancestry and subgenome histories in polyploid species, including allopolyploids common in plants and some animal groups.
• Reticulate phylogenetics: Reconstructs reticulate phylogenies to resolve hybridization and genome-merger events between diploid progenitors and allopolyploids.
• Systematics and comparative studies: Supports resolving genetic relationships between allopolyploids and their diploid ancestors for evolutionary and systematic analyses.

Methodology:

Assigns alleles to diploid progenitor subgenomes using a heuristic MDC-based procedure on multi-locus sequence datasets; applies a consensus procedure to evaluate confidence in allele partitions and phylogenetic inferences; performs simulations of tetra- and hexaploids under completely disomic inheritance and compares reconstructed topologies to MDC species trees based on true allele partitions.