PhyloBot

PhyloBot performs automated phylogenetic inference and ancestral sequence reconstruction to infer ancestral protein sequences and identify evolutionary amino acid changes.

Key Features:

• Automated ancestral sequence reconstruction: Performs phylogenetic ancestral sequence reconstruction to infer ancestral protein sequences.
• Identification of amino acid changes: Detects and reports key amino acid substitutions across evolutionary timescales.
• Ordering evolutionary events: Facilitates ordering of historical events related to the evolution of protein functions.
• Mutational trajectory exploration: Provides interactive computational tools to explore mutational trajectories and evolutionary pathways.
• Ancestral sequence outputs for synthesis: Produces ancestral sequences suitable for synthesis and experimental comparison with extant proteins.
• Software integration: Integrates the software components required for ancestral sequence reconstruction and phylogenetic analysis.
• Implementation and infrastructure: Implemented in Python within the Django web framework and runs on Amazon Web Services elastic cloud computing resources.

Scientific Applications:

• Experimental resurrection of proteins: Enables reconstruction of ancestral sequences for synthesis and experimental comparison with modern proteins.
• Functional evolution analysis: Identifies genetic changes that underlie functional shifts in proteins.
• Hypothesis generation for experimental testing: Generates hypotheses about evolutionary trajectories that can be tested by genetic or biochemical methods.
• Protein-family studies: Applied to investigate the evolution and mechanisms of protein families such as V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases.

Methodology:

Performs phylogenetic ancestral sequence reconstruction, identifies amino acid substitutions, and orders historical functional events; implemented in Python with the Django web framework and executed on Amazon Web Services elastic cloud computing resources.