How to download and install mreps

There are several options:

• The most recommended way is to install it from the mreps GitHub site. For this, run the commands:

  git clone https://github.com/gregorykucherov/mreps.git
  cd mreps
  make

• If you are not comfortable with GitHub, you can download the distribution. To install it, follow the steps:

    tar -xvf mreps-2.6.tar
    cd mreps
    make
  

• For an earlier version of mreps, there are also binaries available for linux, windows, mac os x
• A very old distribution mreps-2.1 is still available. This version can handle the general ascii alphabet, and therefore can still be useful.

How to run it

The usage of mreps is

  mreps [ <options> ] { <sequencefile> | -s <sequence> }

Options

  -from n 	    process starting from position n
  -to n 	    process until position n
  -step n 	    process by sliding windows of size 2*n overlapping by n
 
  -minsize n 	    search for repetitions of size greater or equal to n
  -maxsize n 	    search for repetitions of size smaller or equal to n
  -minp n	    search for repetitions of period greater or equal to n
  -maxp n	    search for repetitions of period smaller or equal to n
  -exp x 	    search for repetitions of exponent greater or equal to x
 
  -res n            resolution parameter
 
  -allowsmall 	    switch off filtering out small repeats
 
  -xmloutput file   output to file in xml format
  -fasta 	    allow DNA sequences in fasta format (option used only with DNA version)
  -noprint 	    output only parameters of repetitions but not the sequences themselves
 
  -v, -vv, -vvv     verbose

Example

  > mreps -res -exp 3.0 -from 10000 -to 12000 -fasta ecolim52.fas

outputs all repeats of exponent >=3 computed with resolution 1 and occurring between positions 10000 and 12000 in the DNA sequence in fasta format stored in file ecolim52.fas

Licence

mreps is distributed under the GNU General Public License

For questions about mreps or for bug reports, please contact