treehouse

treehouse extracts subtrees from large phylogenetic trees to enable focused analysis of evolutionary relationships among specified taxa.

Key Features:

• Subtree extraction: Extracts subtrees from input phylogenies based on a user-specified set of taxa.
• Large-scale phylogeny integration (TreehouseDB): Integrates hosted large-scale phylogenies from TreehouseDB for subtree retrieval.
• Custom phylogeny upload and parsing (userTree): Provides the userTree function to upload and parse custom phylogenetic trees.
• Scalability: Supports extraction from phylogenies that span hundreds to thousands of taxa.
• R implementation: Implemented in the R programming environment to facilitate incorporation into computational workflows.

Scientific Applications:

• Targeted evolutionary analysis: Enables focused analysis of evolutionary relationships among subsets of taxa within large phylogenies.
• Analysis of large genomic phylogenies: Facilitates investigation of evolutionary patterns in phylogenies comprising hundreds to thousands of genomes.

Methodology:

Hosts TreehouseDB large-scale phylogenies, provides a userTree function to upload and parse custom phylogenies, and uses a three-step workflow to retrieve subtrees from a given phylogeny based on a specified set of taxa; implemented in R.