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                                   README 
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Source File: align.c
C library used: BSP (Bulk Synchronous Parallel)

To compile:

  bspcc -o <EXECUTABLE> align.c

To run:

  bsprun <EXECUTAVEL> <N_PROCS> <SEQS1> <SEQS2> <NUMBER_OF_ALIGNMENTS>

  where:
      <EXECUTABLE>: The name of executable to generate.
  
      <N_PROCS>: The number of processes. It has to be a divisor of the 
                 lenght of the DNA sequences.
      
      <SEQS1>: One of the two files of DNA sequences. 
      <SEQS2>: The other file of DNA sequences. <SEQS1> or <SEQS2> may have 
               more than one sequence.
      <NUMBER_OF_ALIGNMENTS>: The number of times in pipeline that the program
                              is performed.

The Program:

  The program align.c calcutes the similaties betwen pairs of DNA sequences.
One of the sequences ir drawn from the file <SEQS1>, and the other from the
file <SEQS2>.
  The program can calculate any number of alignments, defined in <NUMBER_OF_ALIGMENTS>,
since the files <SEQQS1> and <SEQS2> have sufficient number of DNA sequences.
  


Input and Output:


  The files <SEQS1> and <SEQS2> are generated by the program:

    generator.c

  They are the input sequences to the program. To a given <NUMBER_OF_ALIGMENTS>,
there should be at least <NUMBER_OF_ALIGMENTS> in each of the files.
  To generate a file with <n> sequences of size <m> you have to do:
  
    generator <n> <m>
  
  The outputs are printed to the standard output, so redirect it to 
a file.
