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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 must be installed:

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