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Installation notes

RepeatModeler has a number of dependencies. How these are installed are detailed below:


nseg and nmerge (included in nseg) are quite old programs coded in C by NCBI. These were installed on all machines in /usr/local/bin


The same is done with RECON, which consists of the following executables:

  • imagespread
  • eledef
  • eleredef
  • edgeredef
  • famdef

So all these are now available in /usr/local/bin in the nodes as well.


As this also only includes two C-coded executables with quite good names, it is easy enough to install it locally on all the nodes:

  • RepeatScout
  • build_lmer_table

and also the following perl scripts (using the unusual *.prl extension) must be also be installed:

  • filter-stage-1.prl
  • filter-stage-2.prl
  • merge-lmer-tables.prl
  • compare-out-to-gff.prl

RepeatModeler itself

This is quite similar to RepeatMasker, although there is an opportunity to manually edit which is more accurate and convenient than the automatic configure script. Predictably, it will only be active when the tmp extension is hived off.