Mauve¶
Description¶
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.
Run export _JAVA_OPTIONS="-Xmx<MEMORY>" where
Environment Modules¶
Run module spider mauve to find out what environment modules are available for this application.
Environment Variables¶
- HPC_MAUVE_DIR - installation directory
- HPC_MAUVE_BIN - executable directory
- HPC_MAUVE_DOC - documentation directory
Additional Usage Information¶
See using mauve from the command-line for more detailed documentation.
You can also briefly run the main GUI by using X11 Forwarding. See our GUI Programs Help Page for more detailed information.
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".
Categories¶
biology, ngs, genomics