phylogenize

phylogenize performs phylogenetic regression analyses to link microbial genes to environmental prevalence and specificity while accounting for evolutionary relationships among microbes.

Key Features:

• Phylogenetic comparative methods: Implements phylogenetic comparative methods, specifically phylogenetic regression, to control for shared evolutionary history when associating genes with environments.
• Data compatibility: Supports both 16S amplicon and shotgun sequencing data.
• Software integration: Integrates with QIIME 2 and R.
• Visualization capabilities: Provides visualization outputs for interpreting phylogenetic regression results and gene–environment associations.

Scientific Applications:

• Host-associated microbiome analysis: Identifies genes and pathways associated with microbial colonization and specificity in host-associated datasets, demonstrated using Human Microbiome Project data.
• Environmental microbiome studies: Links microbial genes to environmental prevalence and specificity in environmental surveys, demonstrated using Earth Microbiome Project data.
• Cross-platform validation and gene discovery: Produces consistent findings across 16S amplicon and shotgun sequencing and aids identification of known pathways and candidate genes underlying community composition differences.

Methodology:

Performs phylogenetic regression analyses on community composition data to link microbial genes to environmental prevalence or specificity while accounting for phylogenetic relationships among microbes.