zalign(1)
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