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NAME

       zalign - parallel local alignment of biological sequences

SYNOPSIS

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

DESCRIPTION

       zAlign  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



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