ALN README

Welcome to ALN!

ALN is a pairwise sequence aligner.


CONTACT
------- 
  You can contact any of the following developers:

    * Héctor Condori Alagón ([email protected])


DOWNLOAD and BUILDING
---------------------

  ALN is available in in GitHub, so you can download by invoking the following commands:

    $ git clone https://github.com/hcondori/aln.git
    
   In Ubuntu and Debian distributions, you can install dependencies by using theses commands:
    
    $ apt-get install git 
    $ apt-get install g++
    $ apt-get install cmake
    $ apt-get install libboost-program-options-dev

  
  Finally, use CMake to build ALN:

    $ cmake .
    $ make

RUNING
-------

  For command line options invoke:

    $ ./src/aln -h


  In order align sequences, invoke:

      $./src/aln -a file1.fasta -b file2.fasta -o out.txt