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.

mlagan                                           September 2018                                        MLAGAN(1)