phangorn is an R package for phylogenetic reconstruction and analysis. It supports Maximum Likelihood, Maximum Parsimony, distance-based methods, and Hadamard conjugation, enabling researchers to estimate phylogenetic trees and networks, compare trees, perform model selection, and visualize phylogenetic relationships.
Why it stands out:
- Multiple phylogenetic methods (Maximum Likelihood, Maximum Parsimony, distance-based)
- Tree comparison, model selection, and network visualization
- Well-documented with detailed vignettes
- Available on CRAN: install.packages(“phangorn”)
Sustainability Snapshot via Cancer Complexity Toolkit:
- 📚 Strong documentation with README and comprehensive vignettes
- 🔧 Active development (last updated November 2025, 212 stars)
- ✅ Quality indicators: JOSS Score 0.40 | Almanack 0.55
- 🌱 Opportunities for growth: enhanced community guidelines and expanded test coverage
Why this matters:Â phangorn provides a comprehensive suite of phylogenetic methods in R, supporting diverse research needs from tree estimation to network analysis. The “Developing” Almanack status (0.55) and recent updates indicate ongoing maintenance. With availability on CRAN and detailed documentation, phangorn is a reliable tool for phylogenetic analysis in computational biology.
