Rphylip is an R package that acts as a comprehensive programming interface for Joseph Felsenstein’s legacy PHYLIP (Phylogeny Inference Package) software suite. Developed by biologists Liam Revell and Scott Chamberlain, it bridges the gap between traditional, command-line phylogenetic software and the modern R statistical environment.
By migrating roughly 90% of PHYLIP’s capabilities directly into R, the package eliminates manual file manipulation and scales phylogenetic analyses into automated, reproducible workflows. Core Architecture and Automation
Traditionally, executing a PHYLIP analysis required a rigid sequence of console prompts, manual file renames (e.g., changing outfile to infile), and strict text configuration files. Rphylip completely automates this background complexity:
Automated Data I/O: R automatically writes your sequence matrices or distance data into temporary PHYLIP-compatible files.
Background Execution: R calls the native, pre-compiled PHYLIP command-line executables to process the data.
Result Parsing: Output objects (like text logs and Newick tree strings) are immediately read, parsed, and converted back into native R object classes (such as phylo objects for the ape package).
File Cleanup: By default, Rphylip deletes all temporary background input/output files after execution to prevent directory clutter. Key Supported Workflows
Rphylip wraps a broad range of core phylogeny reconstruction and comparative biological methods: Rphylip: an R interface for PHYLIP – ADS
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