Fei Hu1,2, Yu Lin3, Jijun Tang4,5. 1. Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, 300072, China. hufeiyc@gmail.com. 2. Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208, SC, USA. hufeiyc@gmail.com. 3. Department of Computer Science and Engineering, University of California, San Diego, 92093 La Jolla, CA, USA. yul280@ucsd.edu. 4. Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, 300072, China. jtang@ces.sc.edu. 5. Department of Computer Science and Engineering, University of South Carolina, Columbia, 29208, SC, USA. jtang@ces.sc.edu.
Abstract
BACKGROUND: 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: MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO 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 .
BACKGROUND: 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: MLGO (Maximum Likelihood for Gene-Order Analysis) is a web tool for the reconstruction of phylogeny and/or ancestral genomes from gene-order data. MLGO 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 .
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