Mauve

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Link/URL:	Mauve
What:	Constructs multiple genome alignments in the presence of large-scale evolutionary events
Who:	The University of Wisconsin - Madison
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Short Description

Home Page

Mauve running on Mac OS X.

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Mauve is a multiple-genome alignment program and visualizer.

"Mauve is a software

package that attempts to align orthologous and xenologous regions among two or more genome sequences that have undergone

both local and large-scale changes."

Links

Mauve at the Genome Evolution Laboratory: http://gel.ahabs.wisc.edu/mauve/

Requirements

Mauve pre-built binaries are available for Windows, Mac OS X (10.4+), and Linux. You can also download the source code and compile a version yourself.

User notes

• Uses a heuristic anchor-based approach to find local matches, then extending them to a global alignment.
• Relaxes the criteria that the genomes be colinear

• overview
  1. Find local alignments (using multiMUMs)
  2. use the multiMUMs to generate a guide tree (phylogenetic tree)
  3. use a subset of the multiMUMs to use as anchors (called LCBs)
  4. perform recursive anchoring to identifiy more alignment anchors
  5. preform a progressive alignment of each LCB using the guide tree

• inGeno looks like a similar program. Not sure about the differences in methods, though.
  --Daniel 19:11, 8 April 2009 (UTC)

References

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