.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
.TH MPIALIGN "1" "16. Aug 2009" "0.9.1" "User Commands"
.SH NAME
mpialign \- parallel local alignment of biological sequences
.SH SYNOPSIS
.B
mpialign
[\-s scores] [\-S split] [\-H hblk] [\-V vblk] file1 file2
.SH 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.
.SS "General options:"
.TP
\fB\-h\fR
display this help and exit
.TP
\fB\-s\fR <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
.SS "Stage 2 options:"
.TP
\fB\-S\fR <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
.TP
\fB\-H\fR <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
.TP
\fB\-V\fR <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