rotl

rotl interfaces with the Open Tree of Life APIs to query, download, and integrate phylogenetic and taxonomic data within R for phylogenetic, biodiversity, and evolutionary analyses.

Key Features:

• Open Tree of Life API access: Query and download subsets of the synthetic Open Tree of Life and associated taxonomic and published-phylogeny data via the Open Tree of Life APIs.
• Taxonomic standardization and reuse: Retrieve and standardize phylogenetic data to facilitate reuse of published trees that are otherwise available only as images.
• Integration with R data structures: Represent returned phylogenies and taxonomic data using common R data structures for downstream statistical and phylogenetic analyses.
• Data synthesis and combination: Combine OTL-derived phylogenies and taxonomic information with external datasets to support integrated analyses of biodiversity patterns and evolutionary relationships.

Scientific Applications:

• Biodiversity studies: Analyze patterns of taxonomic and phylogenetic diversity across taxa using integrated OTL and external datasets.
• Evolutionary biology: Explore evolutionary relationships and comparative phylogenetic questions using synthetic trees and published phylogenies accessed from OTL.
• Ecological research: Integrate phylogenetic context with ecological data to investigate species–environment relationships and community phylogenetics.

Methodology:

Interact with the Open Tree of Life APIs to query and download subsets of the synthetic OTL, represent results in R data structures, and combine OTL outputs with other datasets.