FUSE-PhyloTree

FUSE-PhyloTree identifies local sequence conservation associated with the different functions of a protein family through phylogenomic analysis.

Key Features:

• Partial local multiple sequence alignment: Identifies local sequence conservation modules within a protein family.
• Three-level phylogenetic reconciliation: Infers the evolution of detected modules and known protein functions within the family's phylogenetic tree.
• Ancestral state reconstruction: Reconstructs ancestral gene functions to annotate gene trees with predicted sequence modules and ancestral gene functions.
• Function-sequence association: Associates functions with specific sequence regions based on their co-emergence.

Scientific Applications:

• Multi-functional protein family analysis: Analyzes paralogous or multi-domain protein families to link functions with sequence conservation modules.
• Gene tree annotation: Produces gene trees annotated with predicted sequence modules and ancestral gene functions.
• Evolutionary inference: Traces the evolution of sequence modules and protein functions through phylogenetic analysis.

Methodology:

FUSE-PhyloTree first identifies local sequence conservation modules using partial local multiple sequence alignment, then infers the evolution of detected modules and known protein functions using three-level phylogenetic reconciliation and ancestral state reconstruction.