Maker

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Description

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

License

GPLv3 and Artistic licence 2.0

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 maker and load default version of maker as

module avail maker/ # list available modules
module load maker   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail maker

and choose explicit version you want to use.

Notice: This application supports parallel computing (MPI, OpenMP) which can have weird consequences. For more details about parallel computing visit the page Parallelization.

Avoid using module maker-2.28, which is incompatible with the current system. Rather use the latest version, maker-2.31.10.

Documentation

Documentation is at http://www.yandell-lab.org/software/maker_docs.html

Homepage

http://www.yandell-lab.org/software/maker.html