The --color option looks best when plotted to a postscript terminal and looks worst when plotted to a png terminal. If the alignment is very sparse, many of the alignments will "disappear" because they are too small to be rendered. If this happens, try editing the gnuplot script to plot with "linespoints" instead of "lines".
The --coverage option is sometimes the only sensible way to plot one vs. The --filter option will throw away sometimes valuable repeat information, but is nonetheless very helpful in cleaning up an otherwise noisy plot. The --layout feature is only meant to be used for multiplots where the two sequence sets are near identical, and even when this is true, the layout algorithm isn't perfect.
The -R -Q options are necessary for any multiplot, otherwise the script won't know how long the sequences are. The sequences will be laid out in the order found in these files and every sequence in --Rfile and --Qfile will be plotted even if no alignments exist.
The --SNP or --breaklen options will change the plot colors so that green is normal and red is highlighted. The first of which is the gnuplot script. This script contains the commands necessary to generate the plot, and refers to the two data files which contain the forward and reverse matches respectively. Line thickness, color, and many other options can be added or removed from the plot by hand editing the gnuplot script.
Examples of the two types of plots are displayed below, the dot plot first, followed by the coverage plot, and finnaly a couple multiplots. For a dot plot, the reference sequence is laid across the x-axis, while the query sequence is on the y-axis. Wherever the two sequences agree, a colored line or dot is plotted.
The forward matches are displayed in red, while the reverse matches are displayed in green. If the two sequences were perfectly identical, a single red line would go from the bottom left to the top right. However, two sequences rarely exhibit this behavior, and in the above plot, multiple gaps and inversions can be identified between these two strains of Helicobacter pylori. This plot was generated from nucmer output, however running mummerplot on a simple match list from mummer would produce similar results, but with more "noise".
In the newer versions, mummerplot plots points at the beginning and end of each line to avoid pixel resolution issues and also uses different plotting colors. Therefore, the output may look slightly different than displayed on these pages. When there are many query sequences mapping to a single reference sequence, it is often helpful to use a coverage or percent identity plot.
This type of plot lays out each of the alignment regions or for show-tiling , the full contigs according to their percent similarity and mapping location to the reference.
Note that since mummer produces nothing but exact matches, only the normalized 1D plot will appear in the figure. Thus, every grid line represents the end of one sequence and the beginning of the next. This allows us to draw every dotplot for the two sequence sets at once, as displayed by the two contig sets in the above left image. With a little shuffling of the order and orientation of the sequences, a more pleasing layout can be obtained as show in the above right image. This is the same contig set as on the left, however the contigs have been reordered and oriented so that the major alignments cluster around the main diagonal of the plot.
This allows for easier browsing of the plot by centralizing the important information, and also highlights contigs that have disagreeing sequences by breaking the diagonal.
Currently a greedy approach is used to perform the layout, and while good at bringing alignments to the diagonal, it does not always produce the optimal ordering. Therefore, a break in the diagonal does not always signal a disagreement between the two sequence sets see the mummerplot --breaklen option for an easy way to highlight assembly discrepancies.
A quick reference guide for interpretting the dot plot is available here. It is handy for identifying the exact location of errors and looking for SNPs between two sequences. All alignments between these two sequences will be displayed.
The -x option applies to amino acid alignments promer output and will only affect the error notations, not the alignment. Output is to stdout and is slightly different depending on the type of alignment, i. Each individual line of the alignment is prefixed with the position of the first base on that line, these positions reference the forward strand of the DNA sequence regardless of alignment type. Perhaps the best way to explain this format is by example, so snippets of the two types of alignments are given below.
It is the most commonly used tool for analyzing the delta files. The -b option alters the output table to only display the location of the aligning regions, not their identity, direction, frame, etc. Also, for protein data, the -b option will collapse all overlapping frames, and list a single encompassing region.
The coverage information added with the -c option is equal to the length of the alignment divided by the length of the sequence. The -T option is different than the -B option because it retain the normal ordering of output columns. The -o annotations will appear in the final column of the output. The descriptions reference the reference sequence, e.
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 sequence. The -b option is useful when the user wishes to identify syntenic 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. The -g option comes in handy when comparing sequences that share a linear alignment relationship, that is there are no rearrangements. Large nsertions, deletions and gaps can then be identified by the break between two adjacent alignments in the output. If there are more than one global alignment that share the same score, then one of them is picked at random to display. This is useful when mapping repetitive reads to a finished sequence.
Some of the described columns, such as percent similarity, will not appear for nucleotide comparisons. When run without the -H or -B options, show-coords prints a header tag for each column; the descriptions of each tag follows. All output coordinates and lengths are relative to the forward strand of the reference DNA sequence. When run with the -B option, output format will consist of 21 tab-delimited columns.
These are as follows:  query sequence ID  date of alignment  length of query sequence  alignment type  reference file  reference sequence ID  start of alignment in the query  end of alignment in the query  start of alignment in the reference  end of alignment in the reference  percent identity  percent similarity  length of alignment in the query  0 for compatibility  0 for compatibility  NULL for compatibility  0 for compatibility  strand of the query  length of the reference sequence  0 for compatibility  and 0 for compatibility.
Polymorphisms are reported one per line, in a delimited fashion similar to show-coords. The -C option is a little confusing, but in simple terms it avoids calling SNPs from repetitive regions. This can be caused by simple repeats, or overlapping alignments caused by tandem repeats that exist in different copy numbers.
Either way, calling SNPs from these regions is questionable, and therefore the -C option should be invoked in most instances. To generate output suitable for further parsing, use the -H -T options.
The [BUFF] output column will refer to the sequence positions requested by the -r -q options, so these options affect more than the order of the output. This option is helpful when the user has a specific alignment they would like to see SNPs from. The '. Output is to stdout and is slightly different depending on which command switches are set. For instance, by default the output is arranged in a table style, however if the -T option is active, the output will be tab-delimited. Also, the sequence files, alignment type and column headers are output by default, however if the -H option is active, the headers will be stripped from the output.
Other options like -l -C -x will add or remove columns from the output. So, for description purposes, all possible column headers will be given and it is up to the user to pair the column header with the column number. The descriptions for each header tag follows. For indels, this position refers to the 1-based position of the first character before the indel, e. For indels on the reverse strand, this position refers to the forward-strand position of the first character before indel on the reverse-strand, e.
All positions are relative to the forward strand of the DNA input sequence, while the [BUFF] distance is relative to the sorted sequence. Given the delta alignment information of a few long reference sequences and many small query contigs, show-tiling will determine the best mapped location of each query 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 to the references. This program is not suitable for "many vs. Primary output will be to stdout.
The -i and -l options filter out all contigs below these cutoffs. The -p option creates a pseudo molecule from the query sequence, and arranges them as the map to the reference. The -v option sets the minimum percent of the query contig that must be covered by aligning bases, while the -V option sets the difference in percent coverage to determine one mapping is better than another. To include the most possible contigs in the tiling, set the -V option to zero and lower the -i and -v options to reasonable values.
For NUCmer data, percent coverage is the non-redundant number of aligning bases divided by the length of the query sequence, while for PROmer data, percent coverage is the extent of the syntenic region divided by the length of the query sequence. The difference being, show-tiling does not penalize a PROmer mapping for having big gaps and small alignments.
The -x option output can be used as input to the TIGR scaffolder "Bambus", for use as contig linking information. With the exception of the output generated by the -t option, all tiling paths include the minimal number of contigs needed to generate the maximum reference coverage.
This means that there may be other, smaller contigs that map to the reference, but because they are shadowed by larger contigs, they are not reported.
The -R option is very useful for maintaining uniform, 'random' coverage of reads when mapping to a reference. Output is to stdout and differs depending on the command line options. Standard output has an 8 column list per mapped contig, separated by the FastA headers of each reference sequence. These columns are as follows:  start in the reference  end in the reference  gap between this contig and the next  length of this contig  alignment coverage of this contig  average percent identity of this contig  contig orientation  contig ID.
Output of the -a and -u options have the same columns as show-coords run with the -THcl options. Output of the -x option follows standard XML format. An example of the standard output of show-tiling follows:. The negative start positions indicate contigs that are wrapping around the origin, since this output was generated with the -c option.
MUMmer's modular design is very beneficial, however it has created a small set of inconveniences. Some modules like mummer have been updated in the recent 3.
Since it is not always possible to update all modules at once, some legacy issues appear. For example, because mgaps was originally written to cluster the output of a matching algorithm that could only handle one reference sequence, its input and output is constrained to handle only a single reference sequence. When mummer was updated in the 3. The same type of annoyance occurs between mummer and gaps , as gaps was originally designed to handle only one reference and only one query sequence.
Such incompatibilities can be inconvenient, but workarounds with stream editors and conversion scripts are common practice by those familiar with MUMmer. Learning more about the output of each program can lead to a better understanding of how the modules communicate with one another and make it possible to format the output of one module so that it can be understood by a legacy module.
If the two sequences contain a different number of copies of the same tandem repeat, these alignment routines will sometimes generate a cluster on either side of the tandem and extend alignments past one another, failing to join them into a single alignment region. This generates two overlapping alignments and makes it difficult to determine what caused this erratic behavior. Any difference in the tandem between the reference and query can be calculated as the difference of the alignment overlap in each sequence.
This bug is more of a nuisance than a critical problem, so a fix is being considered but no timeline has been set for its implementation. The MUMmer programs do not perform validity checking on their inputs. If any part of the package appears to malfunction, please check that the input files are within the constraints of each program i.
This document will be under constant edit, so if you notice any errors please contact us. Stefan's contribution of the new suffix tree code was essential to making MUMmer3.
Agrobacterium tumefaciens Bacillus anthracis Brucella melitensis Buchnera aphidicola Chlamydophila pneumoniae Escherichia coli Helicobacter pylori Mycobacterium tuberculosis Neisseria meningitidis Staphylococcus aureus Streptococcus pyogenes Streptococcus pneumoniae Yersinia pestis multiple species of Agrobacterium tumefaciens Bacillus anthracis Brucella melitensis Buchnera aphidicola Chlamydophila pneumoniae Escherichia coli Helicobacter pylori Mycobacterium tuberculosis Neisseria meningitidis Staphylococcus aureus Streptococcus pyogenes Streptococcus pneumoniae Yersinia pestis.
Total space Mb. Compute MUM-candidates, i. Only match the characters a , c , g , or t case insensitive. Report the query position of a reverse complement match relative to the forward strand of the query sequence. Force 4 column output format that prepends every match line with the reference sequence identifier.
Check that input header labels alternately have the "Reverse" keyword. Use extent of cluster end - start rather than the sum of the match lengths to determine cluster length. Use anchor matches that are unique in the reference but not necessarily unique in the query default behavior.
Distance an alignment extension will attempt to extend poor scoring regions before giving up default Toggle the creation of the delta file. Setting --nodelta prevents the alignment extension step and only outputs the match clusters default --delta.
Maximum diagonal difference factor for clustering, i. Toggle the outward extension of alignments from their anchoring clusters. Setting --noextend will prevent alignment extensions but still align the DNA between clustered matches and create the.
Toggle alignment score optimization. Setting --nooptimize will prevent alignment score optimization and result in sometimes longer, but lower scoring alignments default --optimize. Align only the reverse strand of the query sequence to the forward strand of the reference. Simplify alignments by removing shadowed clusters. Turn this option off if aligning a sequence to itself to look for repeats default --simplify. For every reference-query pair, leave only the alignments which form the longest mutually consistent set.
For each query, leave only the alignments which form the longest consistent set for the query. For each reference, leave only the alignments which form the longest consistent set for the reference. Set the minimum alignment uniqueness, i. Set the maximum alignment overlap for -r and -q options as a percent of the alignment length [0, ], default Set the maximum distance, in base-pairs, between graphically linked matches default Set the magnification at which the figure is rendered, this option will be used when generating PDF or PS files default 1.
Set the number of output files used to partition the output, this is to avoid generating files that are too large to display default Highlight alignments with a breakpoint further than the given distance from the nearest sequence end.
Color plot lines with a percent similarity gradient or turn off all color default color by match direction. Assistant engineers, tape-jockeys, tea makers, gophers, etc. Originally released on 30 August in the U. Reached No. Great Fire. Love On a Farmboy's Wages. Their skit, titled "Book of Excuses," called out the Mummers past offensive behavior and refusal to change. There's a song right? Dem Golden Slippers" is the traditional anthem of the Mummers.
You can expect to hear it by multiple times throughout the parade, as almost every String Band will bust it at at some point. The song is always accompanied by the signature Mummers' Strut. Also, you'll note that many a Mummer is rocking golden shoes -- that's a nod to this song. Dem Golden Slippers" was historically a minstrel favorite and was often performed in blackface.
Mummers have had a bad history concerning blackface, which was officially banned in but has been spotted several times in the years since. Now you know the history, here's how to see the parade. That's the conclusion of the parade. It's a long parade too, with the last group Duffy starting its part of the parade at p. Where are the performances? This year, there are performances at 15th and Market street by all of the divisions.
The string bands will perform as well by Broad and Sansom streets. The final performance by all groups will be at Broad and Carpenter streets. Here's how to watch the parade from home. Don't feel like braving the cold to see the Mummers in person? If you're tuning in from the Philadelphia-area, you can watch the parade on PHL Want to learn more about the Mummers?
Head to the Mummer Museum S. Second St. All the characters are introduced in turn by the Master, St. There is no real interplay between the characters and no combat or cure, so it is more of a "calling-on song" than a play.
Some of the characters dance solos as they are introduced, then all dance a longsword dance together, which climaxes with their swords being meshed together to form a "shield". They each dance with the shield upon their head, then it is laid on the floor and they withdraw their swords to finish the dance.
George makes a short speech to end the performance. Emily Lyle captured the oral history of fourteen people from the lowlands of Scotland recounting their memories of the 'seasonal folk dramas' known as Galoshins. Building on Emily Lyle's outstanding work, Brian Hayward researched the geographical distribution of the play in Scotland, and published  "Galoshins; the Scottish folk play" which includes several maps showing the locations where each version was performed.
These are or were largely across the Central Belt of Scotland, with a strange and unexplained "outlier" at Ballater in Aberdeenshire. Inspired by both these writers, and by folk play workshops at the Scottish Storytelling Centre, the Meadows Mummers are an all-female troupe who perform at local festivals and have recently September returned from performing at the Scots Music School in Barga, Italy. Details about this group can be found on 1 the Scottish Museums and Galleries website, under the sub-heading "theatre", as "Galoshins; tradition with a difference", and 2 in an article for Memoria Imateria, issue 2 on Intangible Cultural Heritage, under the title "Rescuing Galoshins".
This grand parade has history in the old world, and performances in Philadelphia began in the year The parade is related to the Mummers Play tradition from Britain and Ireland. Revivals of this tradition are still celebrated annually in South Gloucestershire, England on Boxing Day along with other locations in England and in parts of Ireland on St. Mumming was used as a means of entertaining at feasts and functions, particular mention is made of one feast where torch bearers lead the same number of mummers in, who would do acrobatics in a variety of costumes, including animal costumes.
At certain feast days e. One practice in example was for a group to visit a local manor, and 'sing out' the lord.
If the lord couldn't match verse for verse the singing group alternating verses , then that lord would have to provide amenities. The formation of roving mumming groups became a popular practice so common it became associated with criminal or lewd behaviour, as the use of masks allowed anonymity; in the time of Henry VIII, it was banned for a period.
On documents such as receipts and bills from the late medieval, come details of mumming parties organised by English monarchs, Henry VIII being known for taking his court mumming incognito. Later, Henry would ban social mumming, and bring the 'masque' form of entertainment to England. It shares common antecedents with the Mummers Play tradition, but in its current form is primarily a house-visiting tradition. Sometime during the Twelve Days of Christmas, usually on the night of the "Old Twelfth" 17 January; equivalent to 6 January in the old Julian calendar , people would disguise themselves with old articles of clothing and visit the homes of their friends and neighbours.
They would at times cover their faces with a hood, scarf, mask or pillowcase to keep their identity hidden. In keeping with the theme of an inversion of rules, and of disguise, crossdressing was a common strategy, and men would sometimes dress as women and women as men. Travelling from house to house, some mummers would carry their own musical instruments to play, sing and dance in the houses they visited.
The host and hostess of these 'mummers parties' would serve a small lunch which could consist of Christmas cake with a glass of syrup or blueberry or dogberry wine. Some mummers would drink a Christmas "grog" before they leave each house, a drink of an alcoholic beverage such as rum or whiskey. One important part of the custom was a guessing game to determine the identity of the visitors. As each mummer was identified, they would uncover their faces, but if their true identity is not guessed they did not have to unmask.
The Mummers Festival takes place throughout December and includes workshops on how to make hobby horses and wren sticks. Mummers plays were performed in Philadelphia in the 18th century as part of a wide variety of working-class street celebrations around Christmas. By the early 19th century, it coalesced with two other New Year customs, shooting firearms, and the Pennsylvania German custom of "belsnickling" adults in masks questioning children about whether they had been good during the previous year.
Through the 19th century, large groups of disguised often in blackface working class young men roamed the streets on New Year's Day, organizing "riotous" processions, firing weapons into the air, and demanding free drinks in taverns, and generally challenging middle and upper-class notions of order and decorum.
Unable to suppress the custom, by the s the city government began to pursue a policy of co-option, requiring participants to join organized groups with designated leaders who had to apply for permits and were responsible for their groups actions."The Mummers' Dance" is a song written, composed, and performed by Canadian Celtic singer Loreena McKennitt, released as a single from the album The Book of Secrets in The song was a surprise hit in the United States [ citation needed ], reaching No. 18 on the Billboard Hot , No. 3 on the Adult Top 40 chart, and No. 17 on the Modern.