IMPACT

IMPACT assesses adaptive evolution in protein-coding genes by integrating multiple sequence alignment, phylogenetic analysis, and protein-structure-informed evaluation of amino acid biochemical constraints.

Key Features:

• Integrated Tools: Integrates ConTest, PhyML, ATV, and Jmol to combine selection testing, phylogenetic inference, tree visualization, and protein-structure analysis.
• Multiple Sequence Alignment Editor: Provides a built-in editor for preparing and editing protein sequence alignments.
• Evolutionary Rate Estimation: Estimates evolutionary rates by evaluating changes in biochemical constraints at the amino acid level.
• Phylogenetic Analysis: Performs phylogenetic analyses using PhyML.
• Protein Structure Analysis: Leverages Jmol for protein structure analyses.
• Selection Detection: Detects negative and positive selection signatures across protein-coding genes.
• Inter-tool Data Integration: Integrates outputs between components to enable combined sequence, phylogeny, and structure analyses.

Scientific Applications:

• Molecular Evolution: Detects and characterizes patterns of negative and positive selection in protein-coding genes.
• Comparative Genomics: Supports comparative analyses of protein sequences across species using alignments and phylogenies.
• Functional Annotation of Protein-Coding Genes: Informs functional inference by combining evolutionary rate estimates and protein-structure information.
• Evolutionary and Ecological Fitness Studies: Identifies adaptive changes relevant to species evolution and ecological fitness.

Methodology:

Integrates ConTest, PhyML, ATV, and Jmol; includes a multiple sequence alignment editor; estimates evolutionary rates by evaluating changes in biochemical constraints at the amino acid level; performs phylogenetic and protein structure analyses; and detects negative and positive selection signatures.