After install go to /opt/RepeatMasker and run the Configuration Program: # perl ./configure * The full path including the name for the TRF program. TRF_PRGM: /usr/bin/trf Add a Search Engine: 1. CrossMatch: you should obtain this yourself, with the proper license, following the instructions here http://www.phrap.org/ 2. RMBlast - NCBI Blast with RepeatMasker extensions: this is available from SBo. 3. HMMER3.1 & DFAM: this is available from SBo. 4. ABBlast/WUBlast (required by DupMasker): you should obtain this yourself, with the proper license, following the instructions here https://blast.advbiocomp.com/licensing/ * RMBlast (rmblastn) INSTALLATION PATH /usr/bin * HMMER INSTALLATION PATH /usr/bin