AMPHORA

AMPHORA automates identification and alignment of 31 conserved bacterial phylogenetic marker genes from protein sequences to support phylogenomic tree construction and phylotype assignment.

Key Features:

• Automated identification of phylogenetic markers: Detects 31 conserved phylogenetic marker genes from input protein sequences.
• High-quality multiple sequence alignments: Produces multiple sequence alignments for each identified marker gene.
• Phylotype assignments: Assigns phylotypes to protein markers for taxonomic classification of microbial sequences.
• High-throughput processing: Demonstrated by construction of a genome tree comprising 578 bacterial species.
• Application to metagenomics: Applied to Sargasso Sea metagenomic data, assigning phylotypes to 18,607 protein markers.

Scientific Applications:

• Phylogenetic tree construction: Supports building phylogenomic trees that resolve evolutionary relationships among bacterial species.
• Metagenomic analysis: Enables phylotype-based characterization of microbial community composition in environmental samples such as the Sargasso Sea.
• Bacterial genomics: Facilitates analysis of bacterial genomes for studies of genetic variation, horizontal gene transfer, and evolutionary dynamics.

Methodology:

Automated identification of conserved marker genes from protein sequences, generation of multiple sequence alignments for those markers, construction of phylogenetic trees, and assignment of phylotypes.