14/09/2006: New version of the LAGAN Toolkit (2.0) is now available from the Download page. This version has numberous bug fixes and new features, please upgrade. The new features are summarized in the README.first file in the Readmes directory.

22/06/2005: In order to provide a more flexible and reliable server for LAGAN users we have teamed up with the VISTA server to produce the alignments and visualizations for all requests to this server. When you click on any of the submission links you will be redirected to special LAGAN/VISTA submission forms, where you can submit your sequences. You will get a link with your results in an e-mail from the VISTA server. In addition to the standard alignments and VISTA PDFs you can now use the dynamic VISTA-browser to view your alignments. It is also no longer required that you specify the tree for Multi-LAGAN - it will be calculated automatically, if you wish.
You can still direct any questions to the LAGAN authors at lagan@cs.stanford.edu

25/05/2004: MLAGAN was used for multiple alignments of human, mouse, rat and macaque genomes based on the PASH anchoring scheme by the BRL group at the Baylor College of Medicine.

25/02/2004: You can now generate LAGAN alignments through Sockeye, a 3D comparative genome browser that provides visualization for Lagan alignments in the context of user-defined or EnsEMBL-imported annotation. Sockeye is developed at the Genome Sciences Centre, Vancouver.


The Lagan Tookit is a set of alignment programs for comparative genomics. The three main components are a pairwise aligner (LAGAN), a multiple aligner (M-LAGAN), and a glocal aligner (Shuffle-LAGAN). All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy. The results of the alignment can be visualized using the VISTA visualization tool.

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