Mauve: Difference between revisions
DanielRenfro (talk | contribs) |
DanielRenfro (talk | contribs) |
||
| Line 49: | Line 49: | ||
* Uses a heuristic anchor-based approach to find local matches, then extending them to a global alignment. | * 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 | * Relaxes the criteria that the genomes be colinear | ||
* overview | |||
*# Find local alignments (using multiMUMs) | |||
*# use the multiMUMs to generate a guide tree (phylogenetic tree) | |||
*# use a subset of the multiMUMs to use as anchors (called LCBs) | |||
*# perform recursive anchoring to identifiy more alignment anchors | |||
*# preform a progressive alignment of each LCB using the guide tree | |||
* [http://ingeno.bioapps.biozentrum.uni-wuerzburg.de/ inGeno] looks like a similar program. Not sure about the differences in methods, though. <br />--[[User:DanielRenfro|Daniel]] 19:11, 8 April 2009 (UTC) | * [http://ingeno.bioapps.biozentrum.uni-wuerzburg.de/ inGeno] looks like a similar program. Not sure about the differences in methods, though. <br />--[[User:DanielRenfro|Daniel]] 19:11, 8 April 2009 (UTC) | ||
Revision as of 19:57, 24 November 2009
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.
<protect>
| Link/URL: | |
|---|---|
| What: |
Constructs multiple genome alignments in the presence of large-scale evolutionary events |
| Who: |
The University of Wisconsin - Madison |
| edit table |
Short Description
Share your knowledge and ideas. How you can help. See Help pages if you need help with using the wiki
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."[1]
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
- Find local alignments (using multiMUMs)
- use the multiMUMs to generate a guide tree (phylogenetic tree)
- use a subset of the multiMUMs to use as anchors (called LCBs)
- perform recursive anchoring to identifiy more alignment anchors
- 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)
See Also
References
See Help:References for how to manage references in EcoliWiki.