NAME

       mlagan - highly parametrizable pairwise global aligner

SYNOPSIS

       mlagan seqfile_1 seqfile_2 [... seqfile_63] [-parameters]

DESCRIPTION

       Lagan  takes local alignments generated by CHAOS as anchors, and limits the search area of
       the Needleman-Wunsch algorithm around these anchors.

       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.

OPTIONS

       -nested : runs improvement in a nested fashion

       -postir : incorporates the final improvement phase

       -lazy : uses lazy mode

       -translate : use translated anchors

       -fastreject : use fast rejection (tuned for human/mouse or closer)

       -verbose : give debug output

       -tree "(...)" : runs with given phylogenetic tree

       -out "filename": outputs to filename

       -nucmatrixfile    "filename":    uses    given    substitution    matrix    instead     of
       $LAGAN_DIR/nucmatrix.txt

       -version : prints version info

       -nested : runs improvement in a nested fashion

       -postir : incorporates the final improvement phase

       -lazy : uses lazy mode

       -translate : use translated anchors

       -fastreject : use fast rejection (tuned for human/mouse or closer)

       -verbose : give debug output

       -tree "(...)" : runs with given phylogenetic tree

       -out "filename": outputs to filename

       -nucmatrixfile     "filename":    uses    given    substitution    matrix    instead    of
       $LAGAN_DIR/nucmatrix.txt

       -version : prints version info

ENVIRONMENT

       The LAGAN_DIR variable specifies the location  of  the  nucmatrix  file.  It  defaults  to
       /usr/lib/lagan, where Debian also place that file.