Phylogeny.fr is a web-based platform designed to facilitate phylogenetic analysis for both non-specialists and experts. The platform transparently chains various programs to automate the process of identifying homologous sequences, multiple alignment, phylogenetic reconstruction, and graphical representation of the inferred tree. It offers three main modes: 'One Click,' 'Advanced,' and 'A la Carte.' The 'One Click' mode provides a ready-to-use pipeline with pre-set parameters, while the 'Advanced' mode allows users to customize parameters, and the 'A la Carte' mode offers more flexibility by allowing users to select and set up specific tools and steps. Phylogeny.fr also includes a fast parallel BLAST module for sequence searching and a suite of standalone phylogenetic programs. The platform supports both DNA and protein sequences and is available at http://www.phylogeny.fr/. The authors highlight the platform's user-friendly interface, robustness, and the ability to handle large datasets efficiently. Future developments include adding new features, improving computational capabilities, and enhancing user interaction.Phylogeny.fr is a web-based platform designed to facilitate phylogenetic analysis for both non-specialists and experts. The platform transparently chains various programs to automate the process of identifying homologous sequences, multiple alignment, phylogenetic reconstruction, and graphical representation of the inferred tree. It offers three main modes: 'One Click,' 'Advanced,' and 'A la Carte.' The 'One Click' mode provides a ready-to-use pipeline with pre-set parameters, while the 'Advanced' mode allows users to customize parameters, and the 'A la Carte' mode offers more flexibility by allowing users to select and set up specific tools and steps. Phylogeny.fr also includes a fast parallel BLAST module for sequence searching and a suite of standalone phylogenetic programs. The platform supports both DNA and protein sequences and is available at http://www.phylogeny.fr/. The authors highlight the platform's user-friendly interface, robustness, and the ability to handle large datasets efficiently. Future developments include adding new features, improving computational capabilities, and enhancing user interaction.