.TH MLAGAN "1" "September 2018" "mlagan" "User Commands"
.SH NAME
mlagan \- highly parametrizable pairwise global aligner
.SH SYNOPSIS
mlagan seqfile_1 seqfile_2 [... seqfile_63] [-parameters]
.SH DESCRIPTION
Lagan takes local alignments generated by CHAOS as anchors, and limits
the search area of the Needleman-Wunsch algorithm around these anchors.
.PP
Multi-LAGAN is a generalization of the pairwise algorithm to multiple
sequence alignment.  M-LAGAN performs progressive pairwise alignments,
guided by a user-specified phylogenetic tree. Alignments are aligned to
other alignments using the sum-of-pairs metric.
.SH OPTIONS
.TP
\fB\-nested\fR : runs improvement in a nested fashion
.TP
\fB\-postir\fR : incorporates the final improvement phase
.TP
\fB\-lazy\fR : uses lazy mode
.TP
\fB\-translate\fR : use translated anchors
.TP
\fB\-fastreject\fR : use fast rejection (tuned for human/mouse or closer)
.TP
\fB\-verbose\fR : give debug output
.TP
\fB\-tree\fR "(...)" : runs with given phylogenetic tree
.TP
\fB\-out\fR "filename": outputs to filename
.TP
\fB\-nucmatrixfile\fR "filename": uses given substitution matrix instead of \fI\,$LAGAN_DIR/nucmatrix.txt\/\fP
.TP
\fB\-version\fR : prints version info
.PP
\fB\-nested\fR : runs improvement in a nested fashion
.TP
\fB\-postir\fR : incorporates the final improvement phase
.TP
\fB\-lazy\fR : uses lazy mode
.TP
\fB\-translate\fR : use translated anchors
.TP
\fB\-fastreject\fR : use fast rejection (tuned for human/mouse or closer)
.TP
\fB\-verbose\fR : give debug output
.TP
\fB\-tree\fR "(...)" : runs with given phylogenetic tree
.TP
\fB\-out\fR "filename": outputs to filename
.TP
\fB\-nucmatrixfile\fR "filename": uses given substitution matrix instead of \fI\,$LAGAN_DIR/nucmatrix.txt\/\fP
.TP
\fB\-version\fR : prints version info
.SH ENVIRONMENT
The LAGAN_DIR variable specifies the location of the nucmatrix file. It
defaults to /usr/lib/lagan, where Debian also place that file.