Actually, RepeatMasker 'is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. So RepeatMasker take the sequences and compare them to a repeat library and finally replace the repeats in your query with 'N'or other non DNA bases.

1. Unpack all softwares
2. Copy TRF - Tandem Repeat Finder, RMBlast, makeblastdb and blastx exceutibles in RepeatMasker bin directory
3. Rename Tandem Repeat Finder to trf
4. In linux terminal, go to the bin directory of Repeatmasker and run

   perl ./configure
   

5. This massage will appear in terminal

   RepeatMasker Configuration Program
   
   This program assists with the configuration of the
   RepeatMasker program.  The next set of screens will ask
   you to enter information pertaining to your system
   configuration.  At the end of the program your RepeatMasker
   installation will be ready to use.
   
   
   
   <PRESS ENTER TO CONTINUE>
   

   Now press enter
6. This massage will appear in terminal

   **PERL PROGRAM**
   
     This is the full path to the Perl interpreter.
     e.g. /usr/local/bin/perl or enter "env" if you prefer to use
     the "/usr/bin/env perl" mechanism to locate perl.
   Enter path [ /usr/bin/perl ]:
   

   Now installer will search for PERL installation location. If it is different from above given path, then give the correct path for PERL to installer and press the enter.
7. This massage will appear in terminal

   **REPEATMASKER INSTALLATION DIRECTORY**
   
     This is the path to the directory where
     the RepeatMasker program has been installed.
   
   Enter path [ /home/sanjay/Desktop/RepeatMasker ]:
   

   Now installer will search for RepeatMasker directory location. If it is different from above given path (I have extracted the downloaded RepeatMasker file on deskop), then give the correct path for RepeatMasker to installer and press the enter.
8. This massage will appear in terminal

   **TRF PROGRAM**
   
     This is the full path to the TRF program.
    This is now used by RepeatMasker to mask simple repeats.
   
   Enter path [  ]:
   

   Now installer will search for Tandem Repeat Finder directory location. Since i have already copied the Tandem Repeat Finder in RepeatMasker directory therefore i will just copy the RepeatMasker directory path that is '/home/sanjay/Desktop/RepeatMasker' for me. If it is different from above given path , then give the correct path for Tandem Repeat Finder to installer and press the enter.
9. This massage will appear in terminal

   Add a Search Engine:
      1. CrossMatch: [ Un-configured ]
      2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]
      3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
      4. HMMER3.1 & DFAM: [ Un-configured ]
   
      5. Done
   
   Enter Selection: 
   
   

   Now installer will search for Sequence Search Engine program. Since i am going to use RMBlast, therefore I will choose 2 and press the enter.
10. This massage will appear in terminal

    **RMBlast (rmblastn) INSTALLATION PATH**
    
      This is the path to the location where
      the rmblastn and makeblastdb programs can be found.
    
    Enter path [  ]: 
    

    Now installer will search for RMBlast directory location. Since i have already copied the RMBlast, makeblastdb and blastx exceutibles in RepeatMasker directory therefore i will just copy the RepeatMasker directory path that is '/home/sanjay/Desktop/RepeatMasker' for me. If it is different from above given path , then give the correct path for Tandem Repeat Finder to installer and press the enter.
11. This massage will appear in terminal

    Building RMBlast frozen libraries..
    
    
    
    Do you want RMBlast to be your default
    search engine for Repeatmasker? (Y/N)  [ Y ]:
    

    Now installer will ask whether you want to use RMblast as your Sequence Search Engine. Press enter.
12. This massage will appear in terminal

    Add a Search Engine:
       1. CrossMatch: [ Un-configured ]
       2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured, Default ]
       3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
       4. HMMER3.1 & DFAM: [ Un-configured ]
    
       5. Done
    Enter Selection:
    

    Type 5 and press enter.
13. This massage will appear in terminal that means you have successfully installed the RepeatMasker on your computer

    -- Setting perl interpreter...
    
    Congratulations!  RepeatMasker is now ready to use.
    The program is installed with a minimal repeat library
    by default.  This library only contains simple, low-complexity,
    and common artefact ( contaminate ) sequences.  These are
    adequate for use with your own custom repeat library.  If you
    plan to search using common species specific repeats you will
    need to obtain the complete RepeatMasker repeat library from
    GIRI ( www.giriinst.org ) and install it in /home/sanjay/Desktop/RepeatMasker-late.
    
    Further documentation on the program may be found here:
      /home/sanjay/Desktop/RepeatMasker-late/repeatmasker.help
    

Uses

1. Copy the downloaded library in Reoeatmasker directory
2. Run repeatmasker by

   perl RepeatMasker