[MUMmer-users] MUMmer moving to SourceForge : Version 3.17 released

[Phillippy, A. <APh...@ti...>]

Dear MUMmer users,
My apologies for the mass email, but sometime in the last 6 years you =
indicated an interest in MUMmer either by signing up for the mailing =
list or by downloading a licensed copy of MUMmer. I believe this is the =
only email ever sent to the mailing list, so I'm sure you will forgive =
me for this one bit of spam.
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There is big news! Along with the latest version release, 3.17, MUMmer =
is now hosted at SourceForge.net. This means you will need to migrate to =
our new (voluntary) mailing lists, so read on to find out how.
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As many of you may know, with the help of Stefan Kurtz from the =
University of Hamburg, MUMmer3 was released as Open Source software last =
year. Dr. Kurtz' contribution was vital in making MUMmer3 Open Source. =
His suffix tree implementation superseded our old code which was =
licensed by Celera Genomics, thus releasing all of MUMmer's licensing =
attachments. Now, in another effort foster collaboration, MUMmer is =
being relocated to the world's largest Open Source community, =
SourceForge.net. Here are some important links to the new MUMmer =
webpages:
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http://mummer.sourceforge.net <http://mummer.sourceforge.net>=20
http://mummer.sourceforge.net/manual =
<http://mummer.sourceforge.net/manual>=20
http://www.sourceforge.net/projects/mummer =
<http://www.sourceforge.net/projects/mummer>=20
http://www.tigr.org/software/mummer =
<http://www.tigr.org/software/mummer>  (will link to sourceforge)
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In addition to having a new homepage, MUMmer also has a formalized =
mailing list system. These lists are advertised and maintained by our =
SourceForge project, and can be subscribed to from our project page:
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http://www.sourceforge.net/projects/mummer/lists
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There is a list for active developers and collaborators, a low-traffic =
list for release notices/announcements, and a high-traffic list for =
questions/help/bug reports etc. Descriptions of each can be found on =
their subscription pages. I assume there are a large portion of outdated =
email addresses on our current mailing list, so IT WILL BE UP TO YOU to =
migrate to the new mailing lists. At the very least, subscribe to =
mum...@li... =
<mailto:mum...@li...>  (from the link above or =
links below) to receive updated announcements and release notices. If =
you do not subscribe to the new mailing list, this will be the last =
email you receive regarding MUMmer.
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http://lists.sourceforge.net/lists/listinfo/mummer-devel
http://lists.sourceforge.net/lists/listinfo/mummer-help
http://lists.sourceforge.net/lists/listinfo/mummer-users
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Finally, myself and the rest of Steven Salzberg's lab are proud to =
announce our new home at the Center for Bioinformatics and Computational =
Biology at the University of Maryland Institute for Advanced Computer =
Studies (CBCB at UMIACS). Please check us out at:
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http://www.cbcb.umd.edu
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The current website is only temporary, so we are working hard to launch =
our new website by the Fall of 2005. Until then, you can browse some of =
our project specific websites such as AMOS, A Modular Open Source =
Assembler:
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http://amos.sourceforge.net
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which is also a SourceForge.net project. Browse around or sign up for =
the appropriate mailing lists if you are interested in more information.
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Thank you for your attention and interest in our software. If you have =
not worked with MUMmer in a while, a lot has changed, so please take the =
time to browse through the documentation =
(http://mummer.sourceforge.net/manual =
<http://mummer.sourceforge.net/manual> ) and familiarize yourself with =
the new tools. If you have worked with MUMmer recently, then take a look =
at the latest release notes below. As always, we urge you to contact us =
with any questions/ideas or if you would like to collaborate with us on =
one of our projects. Please send all correspondence to =
<mum...@li...>
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Best Regards,
-Adam Phillippy
MUMmer SourceForge Administrator
Software Engineer, The Institute for Genomic Research
As of July 1st: Faculty Research Assistant, CBCB UMIACS
As of December 1st: PhD student, University of Maryland

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--=3D=3D-- MUMMER 3.17 RELEASE NOTES --=3D=3D--
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The major focus for the 3.17 release has been on draft sequence =
alignment and SNP detection. A couple of tools, namely 'delta-filter' =
and 'show-snps', were introduced in order to deal with these types of =
alignments. Also, additional functionality was added to the 'mummerplot' =
utility for viewing draft sequence alignments and %identity color =
gradients.
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__delta-filter__
The delta-filter utility has been added to help deal with the sometimes =
overwhelming amount of output produced by the nucmer and promer =
whole-genome alignment utilities. Often, many of the matches produced by =
these tools are repeat-induced and need to be filtered out. The =
delta-filter tool provides various methods for filtering out such =
matches, which can be extremely helpful in deciphering the output of a =
draft sequence alignment, or an alignment between two genomes that have =
undergone numerous macroscopic mutation events such as translocations =
and inversions. Please refer to the manual for more information on how =
to apply this tool, or run 'delta-filter -h' for a very short =
description of how to use the different command switches.
http://mummer.sourceforge.net/manual/#filter =
<http://mummer.sourceforge.net/manual/#filter>=20
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__show-snps__
The show-snps utility has been added as an efficient means to extract =
all single nucleotide polymorphisms (SNPs) from a delta-encoded =
alignment file output by nucmer. Given a delta file, it will report each =
SNP in the alignments, one per line, with supporting information. Paired =
with the appropriate output processing, this tool in conjunction with =
nucmer can lead to a robust and easy to use SNP pipeline for the rapid =
identification and verification of SNPs. Please refer to the manual for =
more information.
http://mummer.sourceforge.net/manual/#snps =
<http://mummer.sourceforge.net/manual/#snps>=20
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__mummerplot__
The mummerplot utility has been around for a while, but has only been =
capable of plotting alignments between two sequences. Additional =
functionality has been added to generate "multiplots" where multiple =
dotplots are stacked in rows and columns corresponding to query and =
reference sequences and all displayed on the screen at once. This proves =
very handy for investigating a draft vs. draft sequence alignment or a =
finished vs. draft sequence alignment. By intelligently ordering the =
rows and columns, we can line up the fragmented matches along the main =
diagonal, thus simulating a standard dotplot. With gnuplot v4.0, mouse =
zooming and coordinate capturing (via mouse double click) are supported, =
which makes these plots much more accessible. There are some example =
images of this in the manual, under the mummerplot section. In addition, =
plots can now be colored by a %identity color gradient or have SNPs =
highlighted directly on the plot.
http://mummer.sourceforge.net/manual/#mummerplot =
<http://mummer.sourceforge.net/manual/#mummerplot>=20
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Finally, a couple bug fixes were applied here and there and a couple =
minor improvements were made, but other than the changes listed above, =
everything else should work as before.