TreeSAPP

TreeSAPP performs tree-based phylogenetic profiling to provide sensitive taxonomic and functional classification of genes, reactions, and pathways from cultivated and uncultivated microorganisms.

Key Features:

• Phylogenetic profiling: Employs linear regression of evolutionary distance against taxonomic rank to place closely related and highly divergent query sequences at appropriate taxonomic levels.
• Quantitative classification: Produces quantitative functional and taxonomic classifications for assembled and unassembled genomic data.
• Support for orthologous groups: Integrates complex reference packages such as orthologous groups with additional phylogenetic information for classification.
• Reference packages for biogeochemical cycles: Leverages reference packages representing coding sequences associated with multiple globally relevant biogeochemical cycles.
• Tree-of-life visualizations: Generates visualizations of the tree of life to explore microbial community structure and ecological roles.

Scientific Applications:

• Microbial biogeochemistry: Improves taxonomic assignment and functional annotation of microorganisms that mediate matter and energy transformations in global biogeochemical cycles.
• Environmental genome analysis: Facilitates characterization of genes, reactions, and pathways from environmental genomes, including taxa underrepresented in reference databases.

Methodology:

Uses linear regression of evolutionary distance against taxonomic rank and reference packages of coding sequences linked to biogeochemical cycles; integrates orthologous-group reference data for quantitative functional and taxonomic classification of assembled and unassembled genomic sequences.