clstutils

clstutils performs taxonomic assignment of sequences by combining phylogenetic placement with pplacer and clustering with clst to assign queries on a reference phylogeny.

Key Features:

• Phylogenetic placement: Uses pplacer to place query sequences onto a reference phylogeny for taxonomic assignment.
• Clustering: Integrates clst to cluster sequences based on phylogenetic proximity.
• High-throughput processing: Supports rapid assignment of large datasets, providing speed and accuracy for high-throughput data.
• Bioconductor interoperability: Operates within the Bioconductor ecosystem for compatibility with R packages and related data structures.

Scientific Applications:

• Microbial ecology: Enables precise taxonomic identification of microbial sequences for community and environmental studies.
• Evolutionary biology: Facilitates placement of sequences to infer evolutionary relationships on reference trees.
• Biodiversity studies: Supports species-level assignments useful for assessing species distributions and ecological interactions.

Methodology:

Query sequences are placed onto a reference phylogeny using pplacer, followed by clustering of placed sequences with clst based on phylogenetic proximity.