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PROGRAM:

NAME

mummer - package for sequence alignment of multiple genomes

SYNOPSIS

mummer-annotate <gapfile><datafile>
combineMUMs <RefSequence><MatchSequences><GapsFile>
dnadiff [options]<reference><query> or [options]-d<deltafile>
exact-tandems <file><min-match-len>
gaps
mapview [options]<coordsfile>[UTRcoords][CDScoords]
mgaps [-d<DiagDiff>][-f<DiagFactor>][-l<MatchLen>][-s<MaxSeparation>]
mummer [options]<reference-file><query-files>
mummerplot [options]<matchfile>
nucmer [options]<Reference><Query>
nucmer2xfig
promer [options]<Reference><Query>
repeat-match [options]<genome-file>
run-mummer1 <fastareference><fastaquery><prefix>[-r]
run-mummer3 <fastareference><multi-fastaquery><prefix>
show-aligns [options]<deltafile><refID><qryID>

Input is the .delta output of either the "nucmer" or the "promer" program passed on the
command line.

Output is to stdout, and consists of all the alignments between the query and reference
sequences identified on the command line.

NOTE: No sorting is done by default, therefore the alignments will be ordered as found in
the <deltafile> input.
show-coords [options]<deltafile>
show-snps [options]<deltafile>
show-tiling [options]<deltafile>

DESCRIPTION

OPTIONS

All tools (exept for gaps) obey to the -h, --help, -V and --version options as one would
expect. This help is excellent and makes these man pages basically obsolete.
combineMUMs Combines MUMs in <GapsFile> by extending matches off ends and between MUMs.
<RefSequence> is a fasta file of the reference sequence. <MatchSequences> is a multi-
fasta file of the sequences matched against the reference

-D Only output to stdout the difference positions
and characters
-n Allow matches only between nucleotides, i.e., ACGTs
-N num Break matches at <num> or more consecutive non-ACGTs
-q tag Used to label query match
-r tag Used to label reference match
-S Output all differences in strings
-t Label query matches with query fasta header
-v num Set verbose level for extra output
-W file Reset the default output filename witherrors.gaps
-x Don't output .cover files
-e Set error-rate cutoff to e (e.g. 0.02 is two percent)
dnadiff Run comparative analysis of two sequence sets using nucmer and its associated
utilities with recommended parameters. See MUMmer documentation for a more detailed
description of the output. Produces the following output files:

.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)

MANDATORY:
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

OPTIONS:
-d|delta Provide precomputed delta file for analysis
-h
--help Display help information and exit
-p|prefix Set the prefix of the output files (default "out")
-V
--version Display the version information and exit

mapview
-h
--help Display help information and exit
-m|mag Set the magnification at which the figure is rendered,
this is an option for fig2dev which is used to generate
the PDF and PS files (default 1.0)
-n|num Set the number of output files used to partition the
output, this is to avoid generating files that are too
large to display (default 10)
-p|prefix Set the output file prefix
(default "PROMER_graph or NUCMER_graph")
-v
--verbose Verbose logging of the processed files
-V
--version Display the version information and exit
-x1 coord Set the lower coordinate bound of the display
-x2 coord Set the upper coordinate bound of the display
-g|ref If the input file is provided by 'mgaps', set the
reference sequence ID (as it appears in the first column
of the UTR/CDS coords file)
-I Display the name of query sequences
-Ir Display the name of reference genes
mummer Find and output (to stdout) the positions and length of all sufficiently long
maximal matches of a substring in <query-file> and <reference-file>

-mum compute maximal matches that are unique in both sequences
-mumcand same as -mumreference
-mumreference compute maximal matches that are unique in
the reference-sequence but not necessarily in the query-sequence
(default)
-maxmatch compute all maximal matches regardless of their uniqueness
-n match only the characters a, c, g, or t
they can be in upper or in lower case
-l set the minimum length of a match
if not set, the default value is 20
-b compute forward and reverse complement matches
-r only compute reverse complement matches
-s show the matching substrings
-c report the query-position of a reverse complement match
relative to the original query sequence
-F force 4 column output format regardless of the number of
reference sequence inputs
-L show the length of the query sequences on the header line
nuncmer
nucmer generates nucleotide alignments between two mutli-FASTA input
files. Two output files are generated. The .cluster output file lists
clusters of matches between each sequence. The .delta file lists the
distance between insertions and deletions that produce maximal scoring
alignments between each sequence.

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

--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)
-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|diagfactor Set the clustering diagonal difference separation factor
(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)

promer
promer generates amino acid alignments between two mutli-FASTA DNA input
files. Two output files are generated. The .cluster output file lists
clusters of matches between each sequence. The .delta file lists the
distance between insertions and deletions that produce maximal scoring
alignments between each sequence. The DNA input is translated into all 6
reading frames in order to generate the output, but the output coordinates
reference the original DNA input.

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

--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, measured in
amino acids (default 60)
-c|mincluster Sets the minimum length of a cluster of matches, measured in
amino acids (default 20)
--[no]delta Toggle the creation of the delta file (default --delta)
--depend Print the dependency information and exit
-d|diagfactor Set the clustering diagonal difference separation factor
(default .11)
--[no]extend Toggle the cluster extension step (default --extend)
-g|maxgap Set the maximum gap between two adjacent matches in a
cluster, measured in amino acids (default 30)
-l|minmatch Set the minimum length of a single match, measured in amino
acids (default 6)
-m|masklen Set the maximum bookend masking lenth, measured in amino
acids (default 8)
-o
--coords Automatically generate the original PROmer1.1 ".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")
-x|matrix Set the alignment matrix number to 1 [BLOSUM 45],
2 [BLOSUM 62] or 3 [BLOSUM 80] (default 2)
repeat-match Find all maximal exact matches in <genome-file>
-E Use exhaustive (slow) search to find matches
-f Forward strand only, don't use reverse complement
-n # Set minimum exact match length to #
-t Only output tandem repeats
-V # Set level of verbose (debugging) printing to #
show-aligns
-h Display help information
-q Sort alignments by the query start coordinate
-r Sort alignments by the reference start coordinate
-w int Set the screen width - default is 60
-x int Set the matrix type - default is 2 (BLOSUM 62),
other options include 1 (BLOSUM 45) and 3 (BLOSUM 80)
note: only has effect on amino acid alignments
show-coords
-b Merges overlapping alignments regardless of match dir
or frame and does not display any idenitity information.
-B Switch output to btab format
-c Include percent coverage information in the output
-d Display the alignment direction in the additional
FRM columns (default for promer)
-g Deprecated option. Please use 'delta-filter' instead
-h Display help information
-H Do not print the output header
-I float Set minimum percent identity to display
-k Knockout (do not display) alignments that overlap
another alignment in a different frame by more than 50%
of their length, AND have a smaller percent similarity
or are less than 75% of the size of the other alignment
(promer only)
-l Include the sequence length information in the output
-L long Set minimum alignment length to display
-o Annotate maximal alignments between two sequences, i.e.
overlaps between reference and query sequences
-q Sort output lines by query IDs and coordinates
-r Sort output lines by reference IDs and coordinates
-T Switch output to tab-delimited format

Input is the .delta output of either the "nucmer" or the "promer" program passed on the
command line.

Output is to stdout, and consists of a list of coordinates, percent identity, and other
useful information regarding the alignment data contained in the .delta file used as
input.

NOTE: No sorting is done by default, therefore the alignments will be ordered as found
in the <deltafile> input.
show-snps
-C Do not report SNPs from alignments with an ambiguous
mapping, i.e. only report SNPs where the [R] and [Q]
columns equal 0 and do not output these columns
-h Display help information
-H Do not print the output header
-I Do not report indels
-l Include sequence length information in the output
-q Sort output lines by query IDs and SNP positions
-r Sort output lines by reference IDs and SNP positions
-S Specify which alignments to report by passing
'show-coords' lines to stdin
-T Switch to tab-delimited format
-x int Include x characters of surrounding SNP context in the
output, default 0

Input is the .delta output of either the nucmer or promer program passed on the command
line.

Output is to stdout, and consists of a list of SNPs (or amino acid substitutions for
promer) with positions and other useful info. Output will be sorted with -r by default
and the [BUFF] column will always refer to the sequence whose positions have been sorted.
This value specifies the distance from this SNP to the nearest mismatch (end of alignment,
indel, SNP, etc) in the same alignment, while the [DIST] column specifies the distance
from this SNP to the nearest sequence end. SNPs for which the [R] and [Q] columns are
greater than 0 should be evaluated with caution, as these columns specify the number of
other alignments which overlap this position. Use -C to assure SNPs are only reported from
unique alignment regions.

show-tiling
-a Describe the tiling path by printing the tab-delimited
alignment region coordinates to stdout
-c Assume the reference sequences are circular, and allow
tiled contigs to span the origin
-g int Set maximum gap between clustered alignments [-1, INT_MAX]
A value of -1 will represent infinity
(nucmer default = 1000)
(promer default = -1)
-i float Set minimum percent identity to tile [0.0, 100.0]
(nucmer default = 90.0)
(promer default = 55.0)
-l int Set minimum length contig to report [-1, INT_MAX]
A value of -1 will represent infinity
(common default = 1)
-p file Output a pseudo molecule of the query contigs to 'file'
-R Deal with repetitive contigs by randomly placing them
in one of their copy locations (implies -V 0)
-t file Output a TIGR style contig list of each query sequence
that sufficiently matches the reference (non-circular)
-u file Output the tab-delimited alignment region coordinates
of the unusable contigs to 'file'
-v float Set minimum contig coverage to tile [0.0, 100.0]
(nucmer default = 95.0) sum of individual alignments
(promer default = 50.0) extent of syntenic region
-V float Set minimum contig coverage difference [0.0, 100.0]
i.e. the difference needed to determine one alignment
is 'better' than another alignment
(nucmer default = 10.0) sum of individual alignments
(promer default = 30.0) extent of syntenic region
-x Describe the tiling path by printing the XML contig
linking information to stdout

Input is the .delta output of the nucmer program, run on very similar sequence data, or
the .delta output of the promer program, run on divergent sequence data.

Output is to stdout, and consists of the predicted location of each aligning query
contig as mapped to the reference sequences. These coordinates reference the extent of
the entire query contig, even when only a certain percentage of the contig was actually
aligned (unless the -a option is used). Columns are, start in ref, end in ref, distance to
next contig, length of this contig, alignment coverage, identity, orientation, and ID
respectively.

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