AmphoraVizu

AmphoraVizu visualizes phylogenetic distributions from AMPHORA2 and AmphoraNet marker-gene outputs to characterize microbial community composition.

Key Features:

• Phylogenetic Visualization: Interprets native AMPHORA2 and AmphoraNet output formats to display phylogenetic distribution within metagenomic samples.
• Customizable Resolution: Allows selection of phylogenetic resolution from superkingdom to species levels for targeted analyses.
• Diverse Chart Types: Produces multiple chart types to represent quantitative relationships in marker-gene-based phylogenetic data.
• Detailed Marker Gene Data: Reports distribution data for all relevant marker genes to inform microbial composition and potential functions in environmental samples.

Scientific Applications:

• Microbial Ecology Studies: Characterizes microbial diversity and relative abundance using marker-gene phylogenetic assignments.
• Environmental Monitoring: Tracks changes in microbial community composition over time or in response to environmental factors.
• Biotechnological Applications: Profiles phylogenetic makeup to inform bioprospecting for novel enzymes or metabolic pathways.

Methodology:

Uses outputs from AMPHORA2 and AmphoraNet, which employ phylogeny-based methods using marker genes to assign partial phylogenetic information to uncharacterized genomic data, and builds on traditional 16S rRNA gene analysis and genome sequence alignments.