Phylogenetics Skills

Expert knowledge for phylogenetic tree analysis, visualization, and annotation management.

ITOL Annotation File Troubleshooting

Common Issue: Species Name Mismatches

Problem: Species in tree file don't match annotation files, causing missing data in ITOL visualization.

Root Causes:

1. Tree processing tools (e.g., TimeTree) may abbreviate species names
2. Capitalization inconsistencies (e.g., Alca_Torda vs Alca_torda)
3. Genus-only names replacing full binomial nomenclature

Solution Workflow: