Hu, FeiLin, YuTang, Jijun2018-11-292018-11-291471-2105http://hdl.handle.net/1885/153022Background The rapid accumulation of whole-genome data has renewed interest in the study of using gene-order data for phylogenetic analyses and ancestral reconstruction. Current software and web servers typically do not support duplication and loss events along with rearrangements. Results MLGOMLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGOMLGO is based on likelihood computation and shows advantages over existing methods in terms of accuracy, scalability and flexibility. Conclusions To the best of our knowledge, it is the first web tool for analysis of large-scale genomic changes including not only rearrangements but also gene insertions, deletions and duplications. The web tool is available from http://www.geneorder.org/server.php.application/pdf201410.1186/s12859-014-0354-62018-11-29