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ZALIGN(1) User Commands ZALIGN(1)

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:

display this help and exit
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:

(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
(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
(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
16. Aug 2009 0.9.1