Phylogeny.fr

Phylogeny.fr is a free web platform for reconstructing and analysing phylogenetic relationships between molecular sequences, launched in 2008 and hosted at LIRMM in Montpellier. It was developed jointly by three French CNRS groups: Information Génomique et Structurale (IGS, Marseille), Méthodes et Algorithmes pour la Bioinformatique (MAB/LIRMM, Montpellier) and Génétique et Evolution des Maladies Infectieuses (GEMI). The project was initiated by Jean-Michel Claverie, with Olivier Gascuel overseeing the phylogenetic components, and it is described in a widely cited 2008 Nucleic Acids Research paper. Its purpose is to make robust phylogenetic workflows accessible to biologists who are not phylogenetics specialists, while still exposing enough configuration for expert use.

Rather than being a single program, Phylogeny.fr transparently chains established third-party tools into a pipeline. A default "One Click" workflow runs MUSCLE for multiple alignment, Gblocks for automatic alignment curation, PhyML for maximum-likelihood tree inference (with aLRT branch support), and TreeDyn for tree rendering. An "Advanced" mode keeps this structure but exposes each program's parameters, and an "A la Carte" mode lets users assemble custom pipelines from a larger toolbox including T-Coffee, ClustalW, BioNJ, parsimony methods, and BLAST-based sequence retrieval. Results are returned as figures (PNG, PDF) plus machine-readable trees and alignments.

Within the graph-data and format-conversion world, Phylogeny.fr is relevant mainly through its Readseq-based data converter, which translates between the sequence-alignment and tree encodings that phylogenetics uses. Trees are handled in format:newick (and TreeDyn's TGF export), while alignments and matrices move between FASTA, PHYLIP, Clustal, and Nexus (format:nexus); the platform does not target richer XML tree exchange such as format:phyloxml or format:nexml. This overlaps in scope with programmatic toolkits like tool:ete and tool:biopython, and with converters such as tool:newick-to-graphml that bridge format:newick into general graph formats.

Its strengths are ease of use, sensible defaults, publication-quality output, and long-running reproducibility as a canonical citation. Limitations are real: it is a hosted web service (no offline/programmatic API for pipelines), input is capped (for example around 200 sequences for MUSCLE/ClustalW and a size-times-taxa-squared ceiling for inference), and the bundled program versions have aged. Its successor, NGPhylogeny.fr, was built on Galaxy to address scalability and modularity.