<< Visualizing multiple genome comparisons with rearrangements and repeats >>


M-GCAT is a tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased. Further details on the M-GCAT algorithm and software can be found in this paper:

T. Treangen and X. Messeguer. M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics 2006, 7:433. [PDF]


The current version is 2.0 beta. Version 1.5 is still being supported, while users of previous versions are recommend to use this most recent version. Most notably this will be the final official release of M-GCAT. Notable new features in release 2.0 include:

  • Genome comparison with repeats (thanks to Repeatoire)
  • Ability to use M-GCAT as a viewer and do the heavy lifting via a remote server (thanks to rpyc)
  • Gene annotation overlay incorporated in M-GCAT Cluster workspace
  • Ability to align genomes via command-line (no need to open the viewer)
  • New multi-coloring feature to quickly visualize rearrangements
      Plus several more additions.


M-GCAT software is both:
  • a command-line genome comparison program written in C++, and
  • an interactive viewer and alignment tool written in python.
Requirements before downloading:
  • PYTHON 2.5 or PYTHON 2.6: http://www.python.org/download
  • TCL/TK 8.3 or newer: http://www.tcl.tk/
There exist precompiled binaries in the following configurations (click on the link to download it):
OS python 2.5 python 2.6 last updated
Windows 32-bit NA zip March 24th, 2010
Linux 64-bit NA tarball March 24th, 2010
Mac Universal tarball tarball March 24th, 2010


M-GCAT takes a set of FastA formatted sequence as input, and outputs an M-GCAT formatted and eXtended Mutil-FastA formatted alignment of the highly conserved regions. Additionally, one can search for intragenomic repeat families using Repeatoire and visualized them in the context of global genome comparison. For further details on running M-GCAT see the user guide for the HTML version of the user guide.


My UPC university email address is not a reliable means of contacting me anymore. Please contact me instead at: email

Site maintained by Todd J Treangen
Last Updated: March 2010