opentree

opentree provides programmatic access to the Open Tree of Life synthesis to retrieve and analyze integrated published phylogenetic trees and unified taxonomic data.

Key Features:

• Python API wrapper: Implements a Python wrapper around the Open Tree of Life web-service APIs to query tree estimates and taxonomic information.
• Integrated phylogenetic and taxonomic data: Exposes the synthesis that integrates published phylogenetic trees with taxonomic data to produce unified evolutionary relationships.
• Programmatic retrieval of tree estimates and taxonomy: Enables retrieval of phylogenetic trees and unified taxonomic information for downstream analysis.

Scientific Applications:

• Phylogenetic estimation across taxa: Used to generate phylogenetic estimates for diverse taxa, including syntheses such as phylogenetic relationships among all bird families.
• Ecological and biodiversity research: Supports studies that capture phylogenetic estimates for taxa observed at sites such as the University of California Merced Vernal Pools and Grassland Reserve.

Methodology:

Leverages the Open Tree of Life synthesis of published phylogenetic trees with taxonomic data and exposes these data via the project's web-service APIs through a Python wrapper.