PHYML Online is a web server that provides access to PHYML, a software for estimating maximum likelihood phylogenies from DNA and protein sequences. It offers various options, including nonparametric bootstrap and estimation of evolutionary parameters, enabling comprehensive phylogenetic analysis of large datasets in reasonable time. The server is available at http://atgc.lirmm.fr/phyml. The paper introduces PHYML Online, a web interface to the PHYML software, which implements a fast and accurate heuristic for maximum likelihood phylogenetic inference. The algorithm is based on a tree-swapping operation called 'nearest neighbour interchange', which defines three possible topological configurations around each internal branch. The algorithm estimates the length of the internal branch that maximizes the likelihood using numerical optimization. The difference in likelihood between the best alternative configuration and the current one defines a score, which determines whether the current configuration can be improved. The algorithm iteratively improves the tree topology and branch lengths, ensuring convergence to an optimal solution. PHYML Online allows users to analyze multiple datasets in a single run and supports multiple input trees for further optimization. It provides options for assessing the reliability of internal branches using nonparametric bootstrap and allows users to save trees and substitution parameters for further analysis. The server processes sequences on a 16-processor IBM computer and sends results via email. Results include a summary of the selected options, maximum likelihood estimates of the substitution model parameters, and the log likelihood of the model. Trees are displayed in NEWICK format and can be viewed through an applet. PHYML Online is available at http://atgc.lirmm.fr/phyml. PHYML can also be downloaded for local installation. The software is implemented in C ANSI and is available under the GNU general public licence. Sources and binaries are available for academic use. The study was funded by the French Ministry of Research and the Réseau des Génopoles. S.G. is supported by a postdoctoral fellowship from the Allan Wilson Centre. Funding for open access publication charges was provided by CNRS-STIC. No conflict of interest is declared.PHYML Online is a web server that provides access to PHYML, a software for estimating maximum likelihood phylogenies from DNA and protein sequences. It offers various options, including nonparametric bootstrap and estimation of evolutionary parameters, enabling comprehensive phylogenetic analysis of large datasets in reasonable time. The server is available at http://atgc.lirmm.fr/phyml. The paper introduces PHYML Online, a web interface to the PHYML software, which implements a fast and accurate heuristic for maximum likelihood phylogenetic inference. The algorithm is based on a tree-swapping operation called 'nearest neighbour interchange', which defines three possible topological configurations around each internal branch. The algorithm estimates the length of the internal branch that maximizes the likelihood using numerical optimization. The difference in likelihood between the best alternative configuration and the current one defines a score, which determines whether the current configuration can be improved. The algorithm iteratively improves the tree topology and branch lengths, ensuring convergence to an optimal solution. PHYML Online allows users to analyze multiple datasets in a single run and supports multiple input trees for further optimization. It provides options for assessing the reliability of internal branches using nonparametric bootstrap and allows users to save trees and substitution parameters for further analysis. The server processes sequences on a 16-processor IBM computer and sends results via email. Results include a summary of the selected options, maximum likelihood estimates of the substitution model parameters, and the log likelihood of the model. Trees are displayed in NEWICK format and can be viewed through an applet. PHYML Online is available at http://atgc.lirmm.fr/phyml. PHYML can also be downloaded for local installation. The software is implemented in C ANSI and is available under the GNU general public licence. Sources and binaries are available for academic use. The study was funded by the French Ministry of Research and the Réseau des Génopoles. S.G. is supported by a postdoctoral fellowship from the Allan Wilson Centre. Funding for open access publication charges was provided by CNRS-STIC. No conflict of interest is declared.