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