PHANTASM

PHANTASM performs phylogenomic analyses of prokaryotic genomes to support taxonomic classification and evolutionary systematics.

Key Features:

• Automation of phylogenomic workflows: Automates workflows from data acquisition to phylogenomic analysis.
• Whole-genome approaches: Leverages whole-genome data to resolve evolutionary relationships at higher resolution than 16S ribosomal RNA (rRNA) gene-based methods.
• Integration with taxonomic databases: Reconciles NCBI Taxonomy with the List of Prokaryotic names with Standing in Nomenclature (LPSN) to align analyses with current nomenclature.
• User control and customization: Provides configurable analysis parameters to tailor analytical steps and workflows.
• Publication-quality outputs: Produces analysis outputs and figures suitable for publication.

Scientific Applications:

• Microbial taxonomy and systematics: Refines taxonomic classification and nomenclature of prokaryotes using genome-scale data.
• Resolving taxonomic ambiguities: Discriminates closely related taxa and resolves ambiguous classifications.
• Species discovery: Supports identification and description of novel prokaryotic species using phylogenomic evidence.
• Evolutionary and ecological studies: Facilitates analyses of microbial diversity, evolution, and ecology through genome-based phylogenies.
• Linking genotype to phenotype: Aids in elucidating the genetic basis of phenotypic traits among prokaryotes via phylogenomic context.

Methodology:

Performs automated data acquisition from genomic databases, processes genomes to conduct phylogenomic analyses, and integrates phylogenomic results with established taxonomic frameworks (including reconciliation with NCBI Taxonomy and LPSN).