RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
See versions of repeatmodeler which are available:
$ module avail repeatmodeler
Load one version into your environment and run it:
$ module load repeatmasker/2.0.1 $ RepeatModeler
Notes from the sysadmin during installation:
$ cd /tmp $ wget http://www.repeatmasker.org/RepeatModeler/RepeatModeler-2.0.1.tar.gz $ tar xf RepeatModeler-2.0.1.tar.gz $ cd RepeatModeler-2.0.1 $ sudo yum install perl-File-Which.noarch $ perl ./configure $ sudo mkdir -p /export/apps/repeatmodeler/2.0.1 $ sudo cp -r * /export/apps/repeatmodeler/2.0.1