Mugsy
Description
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of mugsy and load default version of mugsy as
module avail mugsy/ # list available modules module load mugsy # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail mugsy
and choose explicit version you want to use.
Example
mugsy --directory $SCRATCHDIR --prefix mygenomes xxx1.fasta xxx2.fasta xxx3.fasta
Documentation
Documentation is available at http://mugsy.sourceforge.net/#started.