Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences.
Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.
See using mauve from the command-line on how to use Mauve at the command line. You can also briefly run the main Gui by logging into the gui.rc.ufl.edu server. See GUI_Programs for details on connecting to the gui server.
- To run Mauve gui
- Run '
export _JAVA_OPTIONS="-Xmx<MEMORY>"' where <MEMORY> is the maximum heap memory size to be used by Java for Mauve in Gigabytes (g) or Megabytes (m) before running '
Mauve'. This will override the initial setting of 500m. Examples of memory values in mega- or gigabytes: "1500m" or "2g".