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

0.9.1                                             16. Aug 2009                                         ZALIGN(1)