(Version 3.0 described)

    (Version 2.1 described)

    (Version 1.0 described)

    DESCRIPTION:
    nucmer is for the all-vs-all comparison of nucleotide sequences
    contained in multi-FastA data files.  It is best used for highly
    similar sequence that may have large rearrangements.  Common use
    cases are: comparing two unfinished shotgun sequencing assemblies,
    mapping an unfinished sequencing assembly to a finished genome, and
    comparing two fairly similar genomes that may have large
    rearrangements and duplications.  Please refer to "docs/nucmer.README"
    for more information regarding this script and its output, or type
    'nucmer -h' for a list of its options.

    USAGE:
    nucmer  [options]  <reference>  <query>

    [options]    type 'nucmer -h' for a list of options.
    <reference>  specifies the multi-FastA sequence file that contains
                 the reference sequences, to be aligned with the queries.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences, to be aligned with the references.

    OUTPUT:
    out.delta    the delta encoded alignments between the reference and
                 query sequences.  This file can be parsed with any of
                 the show-* programs which are described in the "RUNNING
                 THE MUMmer UTILITIES" section.

    NOTES:
    All output coordinates reference the forward strand of the involved
    sequence, regardless of the match direction. Also, nucmer now uses
    only matches that are unique in the reference sequence by default,
    use the '--mum' or '--maxmatch' options to change this behavior.

    DESCRIPTION:
    promer is for the protein level, all-vs-all comparison of nucleotide
    sequences contained in multi-FastA data files.  The nucleotide input
    files are translated in all 6 reading frames and then aligned to one
    another via the same methods as nucmer.  It is best used for highly
    divergent sequences that may have moderate to high similarity on the
    protein level.  Common use cases are: identifying syntenic regions
    between highly divergent genomes, comparative genome annotation i.e.
    using an already annotated genome to help in the annotation of a
    newly sequenced genome, and the general comparison of two fairly
    divergent genomes that have large rearrangements and may only be
    similar on the protein level. Please refer to "docs/promer.README"
    for more information regarding this script and its output, or type
    'promer -h' for a list of its options.

    USAGE:
    promer  [options]  <reference>  <query>

    [options]    type 'promer -h' for a list of options.
    <reference>  specifies the multi-FastA sequence file that contains
                 the reference sequences, to be aligned with the queries.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences, to be aligned with the references.

    OUTPUT:
    out.delta    the delta encoded alignments between the reference and
                 query sequences.  This file can be parsed with any of
                 the show-* programs which are described in the "RUNNING
                 THE MUMmer UTILITIES" section.

    NOTES:
    All output coordinates reference the forward strand of the involved
    sequence, regardless of the match direction, and are measured in
    nucleotides with the exception of the delta integers which are
    measured in amino acids (1 delta int = 3 nucleotides). Also, promer
    now uses only matches that are unique in the reference sequence by
    default, use the '--mum' or '--maxmatch' options to change this
    behavior.

    DESCRIPTION:
    This script is taken directly from MUMmer1.0 and is best used to
    align two sequences in which there is high similarity and no re-
    arrangements.  Common use cases are: aligning two finished bacterial
    chromosomes.  Please refer to "docs/run-mummer1.README" for the
    original documentation for this script and its output.

    USAGE:
    run-mummer1  <seq1>  <seq2>  <tag>  [-r]

    <seq1>  specifies the file with the first sequence in FastA format.
            No more than one sequence is allowed.
    <seq2>  specifies the file with the second sequence in FastA format.
            No more than one sequence is allowed.
    <tag>   specifies the prefix to be used for the output files.
    [-r]    is an optional parameter that will reverse complement the
            second sequence.

    OUTPUT:
    out.align       the out.gaps file interspersed with the alignments
                    of the gaps.
    out.errorsgaps  the out.gaps file with an extra column stating the
                    number of errors contained in each gap.
    out.gaps        an ordered (clustered) list of matches with position
                    information, and gap distances between each match.
    out.out         a list of all maximal unique matches between the two
                    input sequences ordered by their start position in the
                    second sequence.

    NOTES:
    All output coordinates reference their respective strand.  This means
    that if the -r switch is active, coordinates that reference the
    second sequence will be relative to the reverse complement of the
    second sequence.  Please use nucmer or promer if this coordinate
    system is confusing.
        Eventually, this script's components will be rewritten to work
    with the new MUMmer format standards and phased out in favor of the
    new components and wrapping script.

    DESCRIPTION:
    This script is the improved version of the MUMmer1.0 run-mummer1
    script.  It uses a new clustering algorithm that appropriately
    handles multiple sequence rearrangements and inversions.  Because
    of this, it can handle more divergent sequences better than
    run-mummer1.  In addition, it allows a multi-FastA query file for
    1-vs-many sequence comparisons.  Please refer to
    "docs/run-mummer3.README" for more detailed documentation of this
    script and its output.

    USAGE:
    run-mummer3  <reference>  <query>  <prefix>

    <reference>  specifies the file with the reference sequence in FastA
                 format.  No more than one sequence is allowed.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences.
    <prefix>     specifies the file prefix for the output files.

    OUTPUT:
    out.align       the out.gaps file interspersed with the alignments
                    of the gaps.
    out.errorsgaps  the out.gaps file with an extra column stating the
                    number of errors contained in each gap.
    out.gaps        an ordered (clustered) list of matches with position
                    information, and gap distances between each match.
    out.out         a list of all maximal unique matches between the two
                    input sequences ordered by their start position in the
                    second sequence.

    NOTES:
    All output coordinates reference their respective strand.  This means
    that for all reverse matches, the coordinates that reference the
    query sequence will be relative to the reverse complement of the
    query sequence.  Please use nucmer or promer if this coordinate
    system is confusing.

    DESCRIPTION:
    This script is a wrapper around nucmer that builds an
    alignment using default parameters, and runs many of nucmer's
    helper scripts to process the output and report alignment
    statistics, SNPs, breakpoints, etc. It is designed for
    evaluating the sequence and structural similarity of two
    highly similar sequence sets. E.g. comparing two different
    assemblies of the same organism, or comparing two strains of
    the same species.  Please refer to "docs/dnadiff.README" for
    more information regarding this script and its output, or type
    'dnadiff -h' for a list of its options.

    USAGE: dnadiff  [options]  <reference>  <query>
      or   dnadiff  [options]  -d <delta file>

    <reference>       Set the input reference multi-FASTA filename
    <query>           Set the input query multi-FASTA filename
       or
    <delta file>      Unfiltered .delta alignment file from nucmer

    OUTPUT:
    .report  - Summary of alignments, differences and SNPs
    .delta   - Standard nucmer alignment output
    .1delta  - 1-to-1 alignment from delta-filter -1
    .mdelta  - M-to-M alignment from delta-filter -m
    .1coords - 1-to-1 coordinates from show-coords -THrcl .1delta
    .mcoords - M-to-M coordinates from show-coords -THrcl .mdelta
    .snps    - SNPs from show-snps -rlTHC .1delta
    .rdiff   - Classified ref breakpoints from show-diff -rH .mdelta
    .qdiff   - Classified qry breakpoints from show-diff -qH .mdelta
    .unref   - Unaligned reference IDs and lengths (if applicable)
    .unqry   - Unaligned query IDs and lengths (if applicable)

    NOTES:
    The report file generated by this script can be useful for
    comparing the differences between two similar genomes or
    assemblies. The other outputs generated by this script are in
    unlabeled tabular format, so please refer to the utility
    specific documentation for interpreting them. A full
    description of the report file is given in "docs/dnadiff.README".

    DESCRIPTION:
    This program reads the output of the 'gaps' program and adds alignment
    information to it.  Part of the original MUMmer1.0 pipeline and can
    only be used on the output of the 'gaps' program.

    USAGE:
    annotate  <gapsfile>  <seq2>

    <gapsfile>  the output of the 'gaps' program.
    <seq2>      the file containing the second sequence in the comparison.

    OUTPUT:
    stdout           the 'gaps' output interspersed with the alignments of
                     the gaps between adjacent MUMs.  An alignment of a
                     gap comes after the second MUM defining the gap, and
                     alignment errors are marked with a '^' character.
    witherrors.gaps  the 'gaps' output with an appended column that lists
                     the number of alignment errors for each gap.

    NOTES:
    This program will eventually be dropped in favor of the combineMUMs
    or nucmer match extenders, but persists for the time being.

    DESCRIPTION:
    This program reads the output of the 'mgaps' program and adds alignment
    information to it.  Part of the MUMmer3.0 pipeline and can only be
    used on the output of the 'mgaps' program. This -D option alters this
    behavior and only outputs the positions of difference, e.g. SNPs.

    USAGE:
    combineMUMs  [options]  <reference>  <query>  <mgapsfile>

    [options]    type 'combineMUMs -h' for a list of options.
    <reference>  the FastA reference file used in the comparison.
    <query>      the multi-FastA reference file used in the comparison.
    <mgapsfile>  the output of the 'mgaps' program run on the match
                 list produced by 'mummer' for the reference and query
                 files.

    OUTPUT:
    stdout           the 'mgaps' output interspersed with the alignments
                     of the gaps between adjacent MUMs.  An alignment of a
                     gap comes after the second MUM defining the gap, and
                     alignment errors are marked with a '^' character.  At
                     the end of each cluster is a summary line (keyword
                     "Region") noting the bounds of the cluster in the
                     reference and query sequences, the total number of
                     errors for the region, the length of the region and
                     the percent error of the region.
    witherrors.gaps  the 'mgaps' output with an appended column that lists
                     the number of alignment errors for each gap.

    DESCRIPTION:

    This program filters a delta alignment file produced by either
    nucmer or promer, leaving only the desired alignments which
    are output to stdout in the same delta format as the
    input. Its primary function is the LIS algorithm which
    calculates the longest increasing subset of alignments. This
    allows for the calculation of a global set of alignments
    (i.e. 1-to-1 and mutually consistent order) with the -g option
    or locally consistent with -1 or -m. Reference sequences can
    be mapped to query sequences with -r, or queries to references
    with -q. This allows the user to exclude chance and repeat
    induced alignments, leaving only the "best" alignments between
    the two data sets. Filtering can also be performed on length,
    identity, and uniquenes.

    USAGE:
    delta-filter  [options]  <deltafile>

    [options]    type 'delta-filter -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  The same delta alignment format as output by nucmer and promer.

    NOTES:
    For most cases the -m option is recommended, however -1 is
    useful for applications that require a 1-to-1 mapping, such as
    SNP finding. Use the -q option for mapping query contigs to
    their best reference location.

    DESCRIPTION:
    This script finds exact tandem repeats in a specified FastA sequence
    file.  It is a post-processor for 'repeat-match' and provides a simple
    interface and output for tandem repeat detection.

    USAGE:
    exact-tandems  <file>  <min match>

    <file>       the single sequence in FastA format to search for repeats.
    <min match>  the minimum match length for the tandems.

    OUTPUT:
    stdout  4 columns, the start of the tandem repeat, the total extent
            of the repeat region, the length of each repetitive unit, and
            to total copies of the repetitive unit involved.

    DESCRIPTION:
    This program reads a list of unique matches between two strings and
    outputs the longest consistent set of matches, followed by all the
    other matches.  Part of the MUMmer1.0 pipeline and the output of the
    'mummer' program needs to be processed (to strip all non-match lines)
    before it can be passed to this program.

    USAGE:
    gaps  <seq1>  [-r]  <  <matchlist>

    <seq1>       The first sequence file that the match list represents.
    <matchlist>  A simple list of matches and NO header lines or other
                 mumbo jumbo.  The columns of the match list should be
                 start in the reference, start in the query, and length
                 of the match.
    [-r]         Simply puts the string "reverse" on the header of the
                 output so 'annotate' knows to reverse the second
                 sequence.

    OUTPUT:
    stdout  an ordered set of the input matches, separated by headers.
            The first set is the longest consistent set of matches and
            the second set is all other matches.

    NOTES:
    This program will eventually be rewritten to be interchangeable with
    'mgaps', so that it may be plugged into the nucmer or promer
    pipelines.

    DESCRIPTION:
    mapview is a utility program for displaying sequence alignments as
    provided by MUMmer, nucmer or promer. This program takes the output
    from these alignment routines and converts it to a FIG, PDF or PS
    file for visual analysis. It can also break the output into multiple
    files for easier viewing and printing. Please refer to
    "docs/mapview.README" for a more detailed description and explination.

    USAGE:
    mapview  [options]  <coords file>  [UTR coords]  [CDS coords]

    [options]       type 'mapview -h' for a list of options.
    <coords file>   show-coords output file
    [UTR coords]    UTR coordinate file in GFF format
    [CDS coords]    CDS coordinate file in GFF format

    OUTPUT:
    Default output format is an xfig file, however this can be changed to
    a postscript of PDF file with the -f option. See 'mapview -h' for a
    list of available formatting options.

    NOTES:
    The produce the coords file input, 'show-coords' must be run with the
    -r -l options. To reduce redundant matches in promer output, run
    show-coords with the -k option. To generate output formats other than
    xfig, the fig2dev utility must be available from the system path. For
    very large reference genomes, FIG format may be the only option that
    will allow the entire display to be stored in one file, as fig2dev has
    problems if the output is too large.

    DESCRIPTION:
    This program reads a list of matches between a single-FastA reference
    and a multi-FastA query file and outputs clusters of matches that lie
    on similar diagonals and within a reasonable distance.  Part of the
    MUMmer3.0 pipeline and the output of 'mummer' need not be processed
    before passing it to this program, so long as 'mummer' was run on a
    1-vs-many or 1-vs-1 dataset.

    USAGE:
    mgaps  [options]  <  <matchlist>

    [options]    type 'mgaps -h' for a list of options.
    <matchlist>  A list of matches separated by their sequence FastA tags.
                 The columns of the match list should be start in
                 reference, start in query, and length of the match.

    OUTPUT:
    stdout  An ordered set of the input matches, separated by headers.
            Individual clusters are separated by a '#' character and
            sets of clusters from different sequences are separated by
            the FastA header tag for the query sequence.

    NOTES:
    It is often very helpful to adjust the clustering parameters.  Check
    'mgaps -h' for the list of parameters and check the source for a
    better idea of how each parameter affects the result.  Often, it is
    helpful to run this program a number of times with different
    parameters until the desired result is achieved.

    DESCRIPTION:
    This is the core program of the MUMmer package.  It is the suffix-tree
    based match finding routine, and the main part of every MUMmer script.
    For a detailed manual describing how to use this program, please refer
    to "docs/maxmat3man.pdf" or in LaTeX format "docs/maxmat3man.tex". By
    default, 'mummer' now finds maximal matches regardless of their
    uniqueness. Limiting the output to only unique matches can be specified
    as a command line switch.

    USAGE:
    mummer  [options]  <reference>  <query> ...

    [options]    type 'mummer -help' for a list of options.
    <reference>  specifies the single or multi-FastA sequence file that
                 contains the reference sequence(s), to be aligned with
                 the queries.
    <query>      specifies the multi-FastA sequence file that contains
                 the query sequences, to be aligned with the references.
                 Multiple query files are allowed, up to 32.

    OUTPUT:
    stdout  a list of exact matches. Varies depending on input, refer to
            the manual specified in the description above.

    NOTES:
    Many thanks to Stefan Kurtz for the latest mummer version. 'mummer'
    now behaves like the old 'mummer2' program by default. The -mum switch
    forces it to behave like 'mummer1', the -mumreference switch forces it
    to behave like 'mummer2' while the -maxmatch switch forces it to behave
    like the old 'max-match' program.

    DESCRIPTION:
    mummerplot is a perl script that generates gnuplot scripts and data
    collections for plotting with the gnuplot utility.  It can generate
    2-d dotplots and 1-d coverage plots for the output of mummer, nucmer,
    promer or show-tiling. It can also color dotplots with an identity
    color gradient.

    USAGE:
    mummerplot  [options]  <matchfile>

    [options]    type 'mummerplot -h' for a list of options.
    <matchfile>  the output of 'mummer', 'nucmer', 'promer', or
                 'show-tiling'. 'mummerplot' will automatically determine
                 the format of the data it was given and produce the plot
                 accordingly.

    OUTPUT:
    out.gp     The gnuplot script, type 'gnuplot out.gp' to evaluate the
               the gnuplot script.
    out.fplot
    out.rplot
    out.hplot  The forward, reverse and highlighted match information for
               plotting with gnuplot.

    out.ps
    out.png    The plotted image file, postscript or png depending on the
               selected terminal type.

    NOTES:
    For alignments with multiple reference or query sequences, be sure to
    use the -r -q or -R -Q options to avoid overlaying multiple plots in
    the same space. For better looking color gradient plots, try the
    postscript terminal and avoid the png terminal.

    DESCRIPTION:
    Script for plotting nucmer hits against a reference sequence. See top
    of script for more information, or see if 'mummerplot' or 'mapview'
    has the functionality required as they are properly maintained.

    DESCRIPTION:
    Finds exact repeats within a single sequence.

    USAGE:
    repeat-match  [options]  <seq>

    [options]  type 'repeat-match -h' for a list of options.
    <seq>      the single sequence in FastA format to search for repeats.

    OUTPUT:
    stdout  3 columns, the start of the first copy of the repeat, the
            start of the second copy of the repeat, and the length of the
            repeat respectively.

    NOTES:
    REPuter (freely available for universities) may be better suited for
    most repeat matching, but 'repeat-match' is open-source and has some
    functionality that REPuter does not so we include it along with the
    MUMmer package.

    DESCRIPTION:
    This program parses the delta alignment output of nucmer and promer
    and displays all of the pairwise alignments from the two sequences
    specified on the command line.

    USAGE:
    show-aligns  [options]  <deltafile>  <IdR>  <IdQ>

    [options]    type 'show-aligns -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.
    <IdR>        the FastA header tag of the desired reference sequence.
    <IdQ>        the FastA header tag of the desired query sequence.

    OUTPUT:
    stdout  each alignment header and footer describes the frame of the
            alignment in each sequence, and the start and finish
            (inclusive) of the alignment in each sequence.  At the
            beginning of each line of aligned sequence are two numbers, the
            top is the coordinate of the first reference base on that line
            and the bottom is the coordinate of the first query base on
            that line.  ALL coordinates reference the forward strand of the
            DNA sequence, even if it is a protein alignment.  A gap caused
            by an insertion or deletion is filled with a '.' character.
            Errors in a DNA alignment are marked with a '^' below the
            error.  Errors in an amino acid alignment are marked with a
            whitespace in the middle consensus line, while matches are
            marked with the consensus base and similarities are marked with
            a '+' in the consensus line.

    DESCRIPTION:
    This program parses the delta alignment output of nucmer and promer
    and displays the coordinates, and other useful information about the
    alignments.

    USAGE:
    show-coords  [options]  <deltafile>

    [options]    type 'show-coords -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  run 'show-coords' without the -H option to see the column
            header tags.  Here is a description of each tag.  Note that
            some of the below tags do not apply to nucmer data, and that
            all coordinates are inclusive and relative to the forward DNA
            strand.

    [S1]    Start of the alignment region in the reference sequence.

    [E1]    End of the alignment region in the reference sequence.

    [S2]    Start of the alignment region in the query sequence.

    [E2]    End of the alignment region in the query sequence.

    [LEN 1] Length of the alignment region in the reference sequence,
    measured in nucleotides.

    [LEN 2] Length of the alignment region in the query sequence, measured
    in nucleotides.

    [% IDY] Percent identity of the alignment, calculated as the
    (number of exact matches) / ([LEN 1] + insertions in the query).

    [% SIM] Percent similarity of the alignment, calculated like the above
    value, but counting positive BLOSUM matrix scores instead of exact
    matches.

    [% STP] Percent of stop codons of the alignment, calculated as
    (number of stop codons) / (([LEN 1] + insertions in the query) * 2).

    [LEN R] Length of the reference sequence.

    [LEN Q] Length of the query sequence.

    [COV R] Percent coverage of the alignment on the reference sequence,
    calculated as [LEN 1] / [LEN R].

    [COV Q] Percent coverage of the alignment on the query sequence,
    calculated as [LEN 2] / [LEN Q].

    [FRM]   Reading frame for the reference sequence and the reading frame
    for the query sequence respectively.  This is one of the columns
    absent from the nucmer data, however, match direction can easily be
    determined by the start and end coordinates.

    [TAGS]  The reference FastA ID and the query FastA ID.

            There is also an optional final column (turned on with the -w
    or -o option) that will contain some 'annotations'. The -o option will
    annotate alignments that represent overlaps between two sequences,
    while the -w option is antiquated and should no longer be used.
    Sometimes, nucmer or promer will extend adjacent clusters past one
    another, thus causing a somewhat redundant output, this option will
    notify users of such rare occurrences.

    NOTES:
    The -c and -l options are useful when comparing two sets of assembly
    contigs, in that these options help determine if an alignment spans an
    entire contig, or is just a partial hit to a different read.  The -b
    option is useful when the user wishes to identify sytenic regions
    between two genomes, but is not particularly interested in the actual
    alignment similarity or appearance.  This option also disregards match
    orientation, so should not be used if this information is needed.

    DESCRIPTION:
    This program classifies alignment breakpoints for the
    quantification of macroscopic differences between two
    genomes. It takes a standard, unfiltered delta file as input,
    determines the best mapping between the two sequence sets, and
    reports on the breaks in that mapping.

    USAGE:
    show-diff  [options]  <deltafile>

    [options]    type 'show-diff -h' for a list of options.
    <deltafile>  the .delta output file from nucmer

    OUTPUT:
    stdout  Classified breakpoints are output one per line with
            the following types and column definitions. The first
            five columns of every row are seq ID, feature type,
            feature start, feature end, and feature length.

    Feature Columns

    IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff
    IDR DUP dup-start dup-end dup-length
    IDR BRK gap-start gap-end gap-length
    IDR JMP gap-start gap-end gap-length
    IDR INV gap-start gap-end gap-length
    IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence

    Feature Types

    [GAP] A gap between two mutually consistent ordered and
    oriented alignments. gap-length-R is the length of the
    alignment gap in the reference, gap-length-Q is the length of
    the alignment gap in the query, and gap-diff is the difference
    between the two gap lengths. If gap-diff is positive, sequence
    has been inserted in the reference. If gap-diff is negative,
    sequence has been deleted from the reference. If both
    gap-length-R and gap-length-Q are negative, the indel is
    tandem duplication copy difference.

    [DUP] A duplicated sequence in the reference that occurs more
    times in the reference than in the query. The coordinate
    columns specify the bounds and length of the
    duplication. These features are often bookended by BRK
    features if there is unique sequence bounding the duplication.

    [BRK] An insertion in the reference of unknown origin, that
    indicates no query sequence aligns to the sequence bounded by
    gap-start and gap-end. Often found around DUP elements or at
    the beginning or end of sequences.

    [JMP] A relocation event, where the consistent ordering of
    alignments is disrupted. The coordinate columns specify the
    breakpoints of the relocation in the reference, and the
    gap-length between them. A negative gap-length indicates the
    relocation occurred around a repetitive sequence, and a
    positive length indicates unique sequence between the
    alignments.

    [INV] The same as a relocation event, however both the
    ordering and orientation of the alignments is disrupted. Note
    that for JMP and INV, generally two features will be output,
    one for the beginning of the inverted region, and another for
    the end of the inverted region.

    [SEQ] A translocation event that requires jumping to a new
    query sequence in order to continue aligning to the
    reference. If each input sequence is a chromosome, these
    features correspond to inter-chromosomal translocations.

    NOTES:
    The estimated number of features, take inversions for example,
    represents the number of breakpoints classified as bordering
    an inversion. Therefore, since there will be a breakpoint at
    both the beginning and the end of an inversion, the feature
    counts are roughly double the number of inversion events. In
    addition, all counts are estimates and do not represent the
    exact number of each evolutionary event.

    Summing the fifth column (ignoring negative values) yeilds an
    estimate of the total inserted sequence in the
    reference. Summing the fifth column after removing DUP
    features yields an estimate of the total amount of unique
    (unaligned) sequence in the reference. Note that unaligned
    sequences are not counted, and could represent additional
    "unique" sequences. Use the 'dnadiff' script if you must
    recover this information. Finally, the -q option switches
    references for queries, and uses the query coordinates for the
    analysis.

    DESCRIPTION:
    This program reports polymorphism contained in a delta encoded
    alignment file output by either nucmer or promer. It catalogs
    all of the single nucleotide polymorphisms (SNPs) and
    insertions/deletions within the delta file
    alignments. Polymorphisms are reported one per line, in a
    delimited fashion similar to show-coords. Pairing this program
    with the appropriate MUMmer tools can create an easy to use
    SNP pipeline for the rapid identification of putative SNPs
    between any two sequence sets.

    USAGE:
    show-snps  [options]  <deltafile>

    [options]    type 'show-snps -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  Standard output has column headers with the following
            meanings. Not all columns will be output by default,
            see 'show-snps -h' for switch to control the output.

    [P1]    SNP position in the reference.

    [SUB]   Character in the reference.

    [SUB]   Character in the query.

    [P2]    SNP position in the query.

    [BUFF]  Distance from this SNP to the nearest mismatch (end of
    alignment, indel, SNP, etc) in the same alignment.

    [DIST]  Distance from this SNP to the nearest sequence end.

    [R]     Number of repeat alignments which cover this reference
    position, >0 means repetitive sequence.

    [Q]     Number of repeat alignments which cover this query
    position, >0 means repetitive sequence.

    [LEN R] Length of the reference sequence.

    [LEN Q] Length of the query sequence.

    [CTX R] Surrounding context sequence in the reference.

    [CTX Q] Surrounding context sequence in the query.

    [FRM]   Reading frame for the reference sequence and the
    reading frame for the query sequence respectively. Simply
    'forward' 1, or 'reverse' -1 for nucmer data.

    [TAGS]  The reference FastA ID and the query FastA ID.

    NOTES:
    It is often helpful to run this with the -C option to assure
    reported SNPs are only reported from uniquely aligned regions.

    DESCRIPTION:
    This program attempts to construct a tiling path out of the query
    contigs as mapped to the reference sequences.  Given the delta
    alignment information of a few long reference sequences and many small
    query contigs, 'show-tiling' will determine the best location on a
    reference for each contig.  Note that each contig may only be tiled
    once, so repetitive regions may cause this program some difficulty.
    This program is useful for aiding in the scaffolding and closure of an
    unfinished set of contigs, if a suitable, high similarity, reference
    genome is available.  Or, if using promer, 'show-tiling' will help
    in the identification of syntenic regions and their contig's mapping
    the the references.

    USAGE:
    show-tiling  [options]  <deltafile>

    [options]    type 'show-tiling -h' for a list of options.
    <deltafile>  the .delta output file from either nucmer or promer.

    OUTPUT:
    stdout  Standard output has 8 columns: start in reference, end in
            reference, gap between this contig and the next, length of this
            contig, alignment coverage of this contig, average percent
            identity of the alignments for this contig, orientation of this
            contig, contig ID. All matches to a reference are headed by the
            FASTA tag of that reference.  Output with the -a option is the
            same as 'show-coords -cl' when run on nucmer data.

    NOTES:
    When run with the -x option, 'show-tiling' will produce an XML output
    format that can be accepted by TIGR's open source scaffolding software
    'Bambus' as contig linking information.