SuperQ

SuperQ computes phylogenetic supernetworks from collections of partial phylogenetic trees to analyze evolutionary relationships and conservation of molecular pathways across species.

Key Features:

• Phylogenetic Super Network Computation: Constructs integrated supernetworks from multiple partial phylogenetic trees to represent combined evolutionary relationships.
• Advanced Query Capabilities: Supports querying complex tree structures and graphs with bounded treewidth for detailed analyses of network topology.
• Non-Exact Match Identification: Implements the color-coding technique (Alon et al., 1995) to detect homeomorphic (non-exact) matches within networks.
• Performance and Efficiency: Executes queries involving up to nine proteins in seconds on current protein interaction network datasets.

Scientific Applications:

• Cross-Species Molecular Pathway Analysis: Enables comparison of molecular pathways across species, exemplified by comparisons of known yeast complexes against a fly protein interaction network to assess conservation.
• Protein Interaction Network Mining: Facilitates mining of protein interaction networks to identify functional relationships and evolutionary patterns.

Methodology:

Computes supernetworks from collections of partial phylogenetic trees, queries molecular interaction databases/networks, and applies the color-coding algorithm to identify homeomorphic matches in bounded-treewidth graphs.