iBIS2Analyzer

iBIS2Analyzer performs phylogeny-driven coevolution analysis of protein families to detect and characterize coevolving residues that indicate physical interactions or functional cooperation.

Key Features:

• Iterative BIS (iBIS2): Implements the iterative BIS algorithm (iBIS2) to enhance detection and analysis of coevolving residues within and between proteins.
• Subtree-focused phylogenetic analysis: Iteratively selects and analyzes subtrees from large phylogenetic trees, including trees with thousands of sequences, to capture lineage-specific coevolution signals.
• Handling of varying evolutionary pressures: Accommodates varying evolutionary pressures by focusing analysis on specific evolutionary lineages.
• Cluster identification and mapping: Identifies clusters of coevolving residues and maps them onto sequences, multiple sequence alignments, or structures.
• Outputs for visualization and comparison: Produces cluster-level outputs suitable for visualization, comparison, and inspection of coevolving residue patterns.

Scientific Applications:

• Protein interaction inference: Infers residue pairs or clusters indicative of physical interactions between amino acids or protein partners.
• Functional site identification: Identifies residues or clusters associated with functional cooperation or conserved functional sites.
• Evolutionary context analysis: Examines how coevolutionary patterns vary across phylogenetic lineages to study evolutionary pressures.
• Structural annotation: Enables mapping of coevolving residues onto 3D structures to aid interpretation of interaction interfaces.

Methodology:

Applies the iterative BIS (iBIS2) method with iterative selection and analysis of subtrees from phylogenetic trees (including thousands of sequences) to detect and cluster coevolving residues, and maps clusters onto sequences, alignments, or structures.