The statistical selection of best-fit models of nucleotide substitution is routine in the phylogenetic analysis of DNA sequence alignments. The programs ModelTest 1 and jModelTest 2 are very popular tools to accomplish this task, with thousands of users and citations. The latter uses PhyML 3 to obtain maximum likelihood estimates of model parameters, and implements different statistical criteria to select among 88 models of nucleotide substitution, including hierarchical and dynamical likelihood ratio tests, Akaike's and Bayesian information criteria (AIC and BIC) and a performance-based decision theory method (see ref. 4 ). jModelTest also provides estimates of model selection uncertainty, parameter importances and model-averaged parameter estimates, including model-averaged phylogenies 4 .However, in recent years the advent of NGS technologies has changed the field, and most researchers are now moving from phylogenetics to phylogenomics, where large sequence alignments typically include hundreds or thousands of loci. Phylogenetic resources therefore need to be adapted to a High Performance Computing (HPC) paradigm, allowing demanding analyses at the genomic level. Here we introduce jModelTest 2, which incorporates more models, new heuristics, efficient technical optimizations and multithreaded and MPI-based implementations for statistical model selection. jModelTest 2 includes several important new features (Supplementary Table 1). We have expanded the set of candidate models from 88 to 1624, resulting from the consideration of the 203 different partitions of the 4 ×4 nucleotide substitution rate matrix (R-matrix) combined with rate variation among sites and equal/unequal base frequencies. Indeed, likelihood computations for a large number of models or for large data sets can be extremely time-consuming, so we have also implemented two different heuristics for the selection of the best-fit model. The first one is a greedy hill-climbing hierarchical clustering that searches the set of 1624 models optimizing at most 288 models (Supplementary Note 1) with almost the same accuracy as an exhaustive search. The second is a heuristic filtering dposada@uvigo.es

Supplementary data are available at Bioinformatics online.

Summary: The selection of models of nucleotide substitution is one of the major steps of modern phylogenetic analysis. Different tools exist to accomplish this task, among which jModelTest 2 (jMT2) is one of the most popular. Still, to deal with large DNA alignments with hundreds or thousands of loci, users of jMT2 need to have access to High Performance Computing clusters, including installation and configuration capabilities, conditions not always met. Here we present jmodeltest.org, a novel web server for the transparent execution of jMT2 across different platforms and for a wide range of users. Its main benefit is straightforward execution, avoiding any configuration/execution issues, and reducing significantly in most cases the time required to complete the analysis.Availability and implementation: jmodeltest.org is accessible using modern browsers, such as Firefox, Chrome, Opera, Safari and IE from http://jmodeltest.org. User registration is not mandatory, but users wanting to have additional functionalities, like access to previous analyses, have the possibility of opening a user account.Contact: info@jmodeltest.org