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.
A simple tutorial is available from here.
Tools to prepare data and view results
You can also use the following tools to prepare gene order data, such as DRIMM, i-ADHoRe, Cyntenator. Biological datasets can be obtained from CoGE.
To view the resulted tree, you can use iTOL.
When you use this server, please provide a valid email so that results can be emailed to you. Sometime you may need to dig your spam folder as the email may be treated as spam by some mail providers.
If you need assistance, please email jtang at cse.sc.edu.