MLGO is a web server designed for genome rearrangement and gene order analysis. It can be used to infer a phylogeny from genome rearrangement and gene order data, and can also obtain an estimation of ancestral genomes, given an input tree. It can handle large scale data with the size ranges from mitochandrial to nuclear genomes. Besides rearrangements, it can also handle gene insertion, deletion and duplication.
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BMC Bioinformatics. 2014 Nov 8;15(1):354. [Epub ahead of print]
MLGO: phylogeny reconstruction and ancestral inference from gene-order data.
Hu F, Lin Y, Tang J.