AvP

AvP automates phylogenetic detection of candidate horizontal gene transfers by retrieving homologous sequences, generating multiple sequence alignments, constructing phylogenies, and analyzing tree topologies to identify HGT events and related evolutionary events such as duplications.

Key Features:

• Automated homolog retrieval: Retrieves homologous sequences for query genes to enable comparative phylogenetic analysis.
• Multiple sequence alignment: Generates multiple sequence alignments (MSAs) for sets of homologous sequences.
• Phylogenetic reconstruction: Constructs phylogenetic trees from MSAs to infer evolutionary relationships.
• Topology analysis: Analyzes tree topologies to distinguish candidate horizontal gene transfers from vertical inheritance.
• Comparative similarity assessment: Compares gene similarity patterns between closely related and distantly related species to detect candidate HGTs.
• Detection of evolutionary events: Integrates phylogenetic evidence to identify related events such as gene duplications alongside HGT candidates.
• High-throughput screening: Enables scalable identification of candidate HGTs across multiple genes or genomes.

Scientific Applications:

• HGT detection: Identification of candidate horizontal gene transfer events across genomes.
• Evolutionary history reconstruction: Elucidation of gene evolutionary trajectories including duplications and transfers using phylogenies.
• Genome evolution studies: Analysis of the impact and dynamics of horizontal gene transfer on genome composition and organismal biology.

Methodology:

Retrieving homologous sequences, generating multiple sequence alignments, constructing phylogenetic trees, analyzing tree topologies, and comparing gene similarity between closely related and distantly related species.