MUMmer

apt-get install csh

cd /root/
wget http://garr.dl.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
tar -xvzf MUMmer3.23.tar.gz
mv MUMmer3.23 /usr/local/
cd /usr/local/MUMmer3.23/
make check
make install
ln -s /usr/local/MUMmer3.23/nucmer /usr/local/bin/
ln -s /usr/local/MUMmer3.23/show-coords /usr/local/bin/
ln -s /usr/local/MUMmer3.23/delta-filter /usr/local/bin/
chown -R root:root /usr/local/MUMmer3.23

nucmer -h

  USAGE: nucmer  [options]  <Reference>  <Query>

  DESCRIPTION:
    nucmer generates nucleotide alignments between two mutli-FASTA input
    files. The out.delta output file lists the distance between insertions
    and deletions that produce maximal scoring alignments between each
    sequence. The show-* utilities know how to read this format.

  MANDATORY:
    Reference       Set the input reference multi-FASTA filename
    Query           Set the input query multi-FASTA filename

  OPTIONS:
    --mum           Use anchor matches that are unique in both the reference
                    and query
    --mumcand       Same as --mumreference
    --mumreference  Use anchor matches that are unique in in the reference
                    but not necessarily unique in the query (default behavior)
    --maxmatch      Use all anchor matches regardless of their uniqueness

    -b|breaklen     Set the distance an alignment extension will attempt to
                    extend poor scoring regions before giving up (default 200)
    --[no]banded    Enforce absolute banding of dynamic programming matrix
                    based on diagdiff parameter EXPERIMENTAL (default no)
    -c|mincluster   Sets the minimum length of a cluster of matches (default 65)
    --[no]delta     Toggle the creation of the delta file (default --delta)
    --depend        Print the dependency information and exit
    -D|diagdiff     Set the maximum diagonal difference between two adjacent
                    anchors in a cluster (default 5)
    -d|diagfactor   Set the maximum diagonal difference between two adjacent
                    anchors in a cluster as a differential fraction of the gap
                    length (default 0.12)
    --[no]extend    Toggle the cluster extension step (default --extend)
    -f
    --forward       Use only the forward strand of the Query sequences
    -g|maxgap       Set the maximum gap between two adjacent matches in a
                    cluster (default 90)
    -h
    --help          Display help information and exit
    -l|minmatch     Set the minimum length of a single match (default 20)
    -o
    --coords        Automatically generate the original NUCmer1.1 coords
                    output file using the 'show-coords' program
    --[no]optimize  Toggle alignment score optimization, i.e. if an alignment
                    extension reaches the end of a sequence, it will backtrack
                    to optimize the alignment score instead of terminating the
                    alignment at the end of the sequence (default --optimize)
    -p|prefix       Set the prefix of the output files (default "out")
    -r
    --reverse       Use only the reverse complement of the Query sequences
    --[no]simplify  Simplify alignments by removing shadowed clusters. Turn
                    this option off if aligning a sequence to itself to look
                    for repeats (default --simplify)
    -V
    --version       Display the version information and exit