RepeatModeler 1.0.7

RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. RepeatModeler 1.0.7 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds RepeatModeler v1.0.7 to your environment"

}

module-whatis "Adds RepeatModeler v1.0.7 to your environment"

set repeatmodeler_107_root /cm/shared/apps/SHARED/RepeatModeler/RepeatModeler-1-0-7/

prepend-path PATH $repeatmodeler_107_root

</source>

Installation details

RepeatModeler requires several packages.

• RepeatMasker; see the relevant Wiki page
• RECON; RECON was compiled from source. Location:

 /cm/shared/apps/WUR/ABGC/RECON/RECON-1.07

• RepeatScout; RepeatScout was compiled from source. Location:

 /cm/shared/apps/WUR/ABGC/RepeatScout/RepeatScout-1

• rmblast; see the RepeatMasker Wiki page
• tandem repeat finder; see the RepeatMasker Wiki page

All dependencies are configured within RepeatModeler; Setting environment variables is therefore not required.

See also

• Globally installed software
• ABGC specific modules

External links

• RepeatModeler page