PhyleasProg

PhyleasProg performs evolutionary analyses of protein-coding sequences from Ensembl protein IDs and species names to infer phylogenetic trees, detect positive and purifying selection with site and branch-site models, map results onto protein sequences and 3D structure models, and analyze gene synteny.

Key Features:

• Input: Accepts lists of Ensembl protein IDs and species names as primary input for analyses.
• Phylogenetic inference: Generates phylogenetic trees to represent evolutionary relationships among the provided sequences.
• Selection analysis: Detects positive and purifying selection using site and branch-site models.
• Sequence visualization: Overlays selection and other analysis results on protein sequences.
• Structural mapping: Projects analysis results onto 3D protein structure models.
• Synteny analysis: Analyzes the synteny environment of related genes to support comparative genomics.

Scientific Applications:

• Comparative genomics and functional inference: Compare homologous sequences across species to identify conserved and divergent functional regions.
• Molecular evolution and selection studies: Characterize patterns of positive and purifying selection at sites and along branches to study adaptive evolution.
• Structure-function integration: Correlate selection signals with 3D structure models to infer structural determinants of function.
• Functional genomics: Support interpretation of high-throughput sequence datasets through phylogenetic and synteny analyses.

Methodology:

Computational methods explicitly include phylogenetic tree reconstruction, site and branch-site selection models, sequence-to-structure mapping, and synteny environment analysis.