NAME

       mpialign - parallel local alignment of biological sequences

SYNOPSIS

       mpialign [-s scores] [-S split] [-H hblk] [-V vblk] file1 file2

DESCRIPTION

       mpiAlign  is  a  local sequence aligner, especially intended for use with large biological DNA sequences,
       with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman exact algorithm with affine  gap
       cost function to perform this task.

   General options:
       -h     display this help and exit

       -s <scores>
              specify a comma-separated list of scores to be used while calculating aligment matrices throughout
              the program. The list must be in  the  format  "-sMATCH,MISMATCH,GAP_OPEN,GAP_EXTENSION"  (without
              quotes),  and  is parsed in this PRECISE order; no spaces are allowed between values. If there are
              any unspecified parameters, these are set to default values  and  a  warning  message  is  issued;
              exceeding parameters are discarded

   Stage 2 options:
       -S <split>
              (mpialign  only)  number of parts in which to split the alignment matrix; after this step a cyclic
              block model is applied, subdividing each part equally between all available nodes

       -H <hblk>
              (mpialign only) number of horizontal subdivisions made by each node to  its  alignment  submatrix;
              since  this value defines block width, a good choice should allow two full matrix lines to fit the
              processor's cache pages, improving algorithm performance

       -V <vblk>
              (mpialign only) number of vertical subdivisions made by each node to its alignment submatrix; this
              value directly affects the amount of internode communication and is used ONLY if 'split' is set to
              1, otherwise it is set to the number of available nodes