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

0.9.1                                             16. Aug 2009                                       MPIALIGN(1)