biogeobearslisted

# BioGeoBEARS Biogeographic Analysis ## Overview BioGeoBEARS (BioGeography with Bayesian and Likelihood Evolutionary Analysis in R Scripts) performs probabilistic inference of ancestral geographic ranges on phylogenetic trees. This skill helps set up complete biogeographic analyses by: 1. Validating and reformatting input files (phylogenetic tree and geographic distribution data) 2. Generating organized analysis folder structure 3. Creating customized RMarkdown analysis scripts 4. Guiding users through parameter selection and model choices 5. Producing publication-ready visualizations ## When to Use This Skill Use this skill when users request: - "Analyze biogeography on my phylogeny" - "Reconstruct ancestral ranges for my species" - "Run BioGeoBEARS analysis" - "Which areas did my ancestors occupy?" - "Test biogeographic models (DEC, DIVALIKE, BAYAREALIKE)" The skill triggers when users mention phylogenetic biogeography, ancestral area reconstruction, or provide tree + distribution data. ## Required Inputs Users must provide: 1. **Phylogenetic tree** (Newick format, .nwk, .tre, or .tree file) - Must be rooted - Tip labels will be matched to geography file - Branch lengths required 2. **Geographic distribution data** (any tabular format) - Species names (matching tree tips) - Presence/absence data for different geographic areas - Can be CSV, TSV, Excel, or already in PHYLIP format ## Workflow ### Step 1: Gather Information When a user requests a