mummer-users — For users of the MUMmer software. Release notices, etc.

Re: [MUMmer-users] Getting started -- Looks like the build instructions are broken

[Adam P. <aph...@gm...>]

Hi Josh,
Yes, the mummer build process is in need of an update, but it should still
work. Some helper binaries are compiled in the directory:

/ext/repo/MUMmer/MUMmer/aux_bin/

It appears to have trouble creating the first binary in this directory.
Does that aux_bin directory exist, and do you have write access to it?

Best,
-Adam


On Thu, Jul 9, 2015 at 6:33 PM, Joshua Marshall <jrm...@mt...> wrote:

> Hello all,
>
> I'm getting started with the coding portion of my summer research and the
> MUMmer base package looks like the best piece of FOSS software and possibly
> all software available to my needs.  I'm getting started, but it appears
> that the current build  instructions at
> http://mummer.sourceforge.net/manual/#compilation are incorrect or
> invalid with the following output being generated
>
> cd /ext/repo/MUMmer/MUMmer/src/kurtz; make mummer
> make[1]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz'
> cd libbasedir; make libbase.a
> make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/libbasedir'
> /usr/bin/gcc -O3   -c -o cleanMUMcand.o cleanMUMcand.c
> /usr/bin/gcc -O3   -c -o clock.o clock.c
> /usr/bin/gcc -O3   -c -o mapfile.o mapfile.c
> /usr/bin/gcc -O3   -c -o multiseq.o multiseq.c
> /usr/bin/gcc -O3   -c -o procopt.o procopt.c
> /usr/bin/gcc -O3   -c -o safescpy.o safescpy.c
> /usr/bin/gcc -O3   -c -o seterror.o seterror.c
> /usr/bin/gcc -O3   -c -o space.o space.c
> ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o
> safescpy.o seterror.o space.o
> ar: creating libbase.a
> a - cleanMUMcand.o
> a - clock.o
> a - mapfile.o
> a - multiseq.o
> a - procopt.o
> a - safescpy.o
> a - seterror.o
> a - space.o
> make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/libbasedir'
> cd streesrc; make libstree.a
> make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/streesrc'
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o construct.o
> construct.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o access.o access.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o scanpref.o scanpref.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o linkloc.o linkloc.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o depthtab.o depthtab.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o ex2leav.o ex2leav.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o dfs.o dfs.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o overmax.o overmax.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o oversucc.o oversucc.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o addleafcount.o
> addleafcount.c
> /usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o iterator.o iterator.c
> ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o
> ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o
> ar: creating libstree.a
> a - construct.o
> a - access.o
> a - scanpref.o
> a - linkloc.o
> a - depthtab.o
> a - ex2leav.o
> a - dfs.o
> a - overmax.o
> a - oversucc.o
> a - addleafcount.o
> a - iterator.o
> make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/streesrc'
> cd mm3src; make mummer
> make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/mm3src'
> /usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o maxmat3.o maxmat3.c
> /usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o maxmatopt.o
> maxmatopt.c
> /usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o maxmatinp.o
> maxmatinp.c
> /usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o findmumcand.o
> findmumcand.c
> /usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o findmaxmat.o
> findmaxmat.c
> /usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o procmaxmat.o
> procmaxmat.c
> /usr/bin/gcc  maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
> procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \
> -o /ext/repo/MUMmer/MUMmer/mummer; chmod 755 /ext/repo/MUMmer/MUMmer/mummer
> make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/mm3src'
> make[1]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz'
> cd /ext/repo/MUMmer/MUMmer/src/tigr; make all
> make[1]: Entering directory '/ext/repo/MUMmer/MUMmer/src/tigr'
> /usr/bin/g++ -O3 tigrinc.cc -c -o tigrinc.o
> /usr/bin/g++ -O3 annotate.cc tigrinc.o -o
> /ext/repo/MUMmer/MUMmer/annotate; chmod 755 /ext/repo/MUMmer/MUMmer/annotate
> /usr/bin/g++ -O3 combineMUMs.cc tigrinc.o -o
> /ext/repo/MUMmer/MUMmer/combineMUMs; chmod 755
> /ext/repo/MUMmer/MUMmer/combineMUMs
> combineMUMs.cc:26:38: warning: deprecated conversion from string constant
> to ‘char*’ [-Wwrite-strings]
>  #define  DEFAULT_ERROR_FILE_NAME     "witherrors.gaps"
>                                       ^
> combineMUMs.cc:109:27: note: in expansion of macro
> ‘DEFAULT_ERROR_FILE_NAME’
>  char  * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
>                            ^
> combineMUMs.cc:135:24: warning: deprecated conversion from string constant
> to ‘char*’ [-Wwrite-strings]
>  char  * Query_Suffix = "Query";
>                         ^
> combineMUMs.cc:145:22: warning: deprecated conversion from string constant
> to ‘char*’ [-Wwrite-strings]
>  char  * Ref_Suffix = "Ref";
>                       ^
> /usr/bin/g++ -O3 delta.cc -c -o delta.o
> /usr/bin/g++ -O3 delta-filter.cc tigrinc.o delta.o -o
> /ext/repo/MUMmer/MUMmer/delta-filter; chmod 755
> /ext/repo/MUMmer/MUMmer/delta-filter
> /usr/bin/g++ -O3 gaps.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/gaps; chmod
> 755 /ext/repo/MUMmer/MUMmer/gaps
> /usr/bin/g++ -O3 mgaps.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/mgaps;
> chmod 755 /ext/repo/MUMmer/MUMmer/mgaps
> mgaps.cc: In function ‘int Process_Cluster(Match_t*, int, char*)’:
> mgaps.cc:533:18: warning: deprecated conversion from string constant to
> ‘char*’ [-Wwrite-strings]
>             label = "#\n";
>                   ^
> mgaps.cc: In function ‘void Process_Matches(Match_t*, int, char*)’:
> mgaps.cc:620:17: warning: deprecated conversion from string constant to
> ‘char*’ [-Wwrite-strings]
>            label = "#\n";
>                  ^
> /usr/bin/g++ -O3 sw_align.cc -c -o sw_align.o
> /usr/bin/g++ -O3 postnuc.cc tigrinc.o sw_align.o -o
> /ext/repo/MUMmer/MUMmer/aux_bin/postnuc; chmod 755
> /ext/repo/MUMmer/MUMmer/aux_bin/postnuc
> /usr/bin/ld: cannot open output file
> /ext/repo/MUMmer/MUMmer/aux_bin/postnuc: No such file or directory
> collect2: error: ld returned 1 exit status
> chmod: cannot access ‘/ext/repo/MUMmer/MUMmer/aux_bin/postnuc’: No such
> file or directory
> Makefile:69: recipe for target 'postnuc' failed
> make[1]: *** [postnuc] Error 1
> make[1]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/tigr'
> Makefile:125: recipe for target 'tigr' failed
> make: *** [tigr] Error 2
>
>
> Before I go in and try to fix what shouldn't be fixed, has anyone else had
> this issue and if so how was it resolved?  If not, when I get the fixes
> made, what is the patch submission policy?
>
>
> Thanks,
> Josh Marshall
>
>
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>
>

[MUMmer-users] Getting started -- Looks like the build instructions are broken

[Joshua M. <jrm...@mt...>]

Hello all,

I'm getting started with the coding portion of my summer research and the
MUMmer base package looks like the best piece of FOSS software and possibly
all software available to my needs.  I'm getting started, but it appears
that the current build  instructions at
http://mummer.sourceforge.net/manual/#compilation are incorrect or invalid
with the following output being generated

cd /ext/repo/MUMmer/MUMmer/src/kurtz; make mummer
make[1]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz'
cd libbasedir; make libbase.a
make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/libbasedir'
/usr/bin/gcc -O3   -c -o cleanMUMcand.o cleanMUMcand.c
/usr/bin/gcc -O3   -c -o clock.o clock.c
/usr/bin/gcc -O3   -c -o mapfile.o mapfile.c
/usr/bin/gcc -O3   -c -o multiseq.o multiseq.c
/usr/bin/gcc -O3   -c -o procopt.o procopt.c
/usr/bin/gcc -O3   -c -o safescpy.o safescpy.c
/usr/bin/gcc -O3   -c -o seterror.o seterror.c
/usr/bin/gcc -O3   -c -o space.o space.c
ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o
safescpy.o seterror.o space.o
ar: creating libbase.a
a - cleanMUMcand.o
a - clock.o
a - mapfile.o
a - multiseq.o
a - procopt.o
a - safescpy.o
a - seterror.o
a - space.o
make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/libbasedir'
cd streesrc; make libstree.a
make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/streesrc'
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o construct.o construct.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o access.o access.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o scanpref.o scanpref.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o linkloc.o linkloc.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o depthtab.o depthtab.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o ex2leav.o ex2leav.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o dfs.o dfs.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o overmax.o overmax.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o oversucc.o oversucc.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o addleafcount.o
addleafcount.c
/usr/bin/gcc -O3 -I../libbasedir -DSTREEHUGE   -c -o iterator.o iterator.c
ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o
ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o
ar: creating libstree.a
a - construct.o
a - access.o
a - scanpref.o
a - linkloc.o
a - depthtab.o
a - ex2leav.o
a - dfs.o
a - overmax.o
a - oversucc.o
a - addleafcount.o
a - iterator.o
make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/streesrc'
cd mm3src; make mummer
make[2]: Entering directory '/ext/repo/MUMmer/MUMmer/src/kurtz/mm3src'
/usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o maxmat3.o maxmat3.c
/usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o maxmatopt.o
maxmatopt.c
/usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o maxmatinp.o
maxmatinp.c
/usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o findmumcand.o
findmumcand.c
/usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o findmaxmat.o
findmaxmat.c
/usr/bin/gcc -O3 -I../libbasedir -I../streesrc   -c -o procmaxmat.o
procmaxmat.c
/usr/bin/gcc  maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o
procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \
-o /ext/repo/MUMmer/MUMmer/mummer; chmod 755 /ext/repo/MUMmer/MUMmer/mummer
make[2]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz/mm3src'
make[1]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/kurtz'
cd /ext/repo/MUMmer/MUMmer/src/tigr; make all
make[1]: Entering directory '/ext/repo/MUMmer/MUMmer/src/tigr'
/usr/bin/g++ -O3 tigrinc.cc -c -o tigrinc.o
/usr/bin/g++ -O3 annotate.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/annotate;
chmod 755 /ext/repo/MUMmer/MUMmer/annotate
/usr/bin/g++ -O3 combineMUMs.cc tigrinc.o -o
/ext/repo/MUMmer/MUMmer/combineMUMs; chmod 755
/ext/repo/MUMmer/MUMmer/combineMUMs
combineMUMs.cc:26:38: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
 #define  DEFAULT_ERROR_FILE_NAME     "witherrors.gaps"
                                      ^
combineMUMs.cc:109:27: note: in expansion of macro ‘DEFAULT_ERROR_FILE_NAME’
 char  * Error_File_Name = DEFAULT_ERROR_FILE_NAME;
                           ^
combineMUMs.cc:135:24: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
 char  * Query_Suffix = "Query";
                        ^
combineMUMs.cc:145:22: warning: deprecated conversion from string constant
to ‘char*’ [-Wwrite-strings]
 char  * Ref_Suffix = "Ref";
                      ^
/usr/bin/g++ -O3 delta.cc -c -o delta.o
/usr/bin/g++ -O3 delta-filter.cc tigrinc.o delta.o -o
/ext/repo/MUMmer/MUMmer/delta-filter; chmod 755
/ext/repo/MUMmer/MUMmer/delta-filter
/usr/bin/g++ -O3 gaps.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/gaps; chmod
755 /ext/repo/MUMmer/MUMmer/gaps
/usr/bin/g++ -O3 mgaps.cc tigrinc.o -o /ext/repo/MUMmer/MUMmer/mgaps; chmod
755 /ext/repo/MUMmer/MUMmer/mgaps
mgaps.cc: In function ‘int Process_Cluster(Match_t*, int, char*)’:
mgaps.cc:533:18: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
            label = "#\n";
                  ^
mgaps.cc: In function ‘void Process_Matches(Match_t*, int, char*)’:
mgaps.cc:620:17: warning: deprecated conversion from string constant to
‘char*’ [-Wwrite-strings]
           label = "#\n";
                 ^
/usr/bin/g++ -O3 sw_align.cc -c -o sw_align.o
/usr/bin/g++ -O3 postnuc.cc tigrinc.o sw_align.o -o
/ext/repo/MUMmer/MUMmer/aux_bin/postnuc; chmod 755
/ext/repo/MUMmer/MUMmer/aux_bin/postnuc
/usr/bin/ld: cannot open output file
/ext/repo/MUMmer/MUMmer/aux_bin/postnuc: No such file or directory
collect2: error: ld returned 1 exit status
chmod: cannot access ‘/ext/repo/MUMmer/MUMmer/aux_bin/postnuc’: No such
file or directory
Makefile:69: recipe for target 'postnuc' failed
make[1]: *** [postnuc] Error 1
make[1]: Leaving directory '/ext/repo/MUMmer/MUMmer/src/tigr'
Makefile:125: recipe for target 'tigr' failed
make: *** [tigr] Error 2


Before I go in and try to fix what shouldn't be fixed, has anyone else had
this issue and if so how was it resolved?  If not, when I get the fixes
made, what is the patch submission policy?


Thanks,
Josh Marshall

[MUMmer-users] is a bug?

[guanhui b. <gua...@gm...>]

hello, when i used Mummer to align a sequence to a contigs, using the
following commond
"/var/data/MUMmer3.21/nucmer --prefix=$1 $3 $2
/var/data/MUMmer3.21/delta-filter -r -q $1.delta > $1.filter
/var/data/MUMmer3.21/show-coords -rcl $1.delta > $1.coords"
the coords file is empty. but  it has two hits by blast . is a bug of
Mummer?
thanks.
-- 
Yours, Guanhui Bao

Institute of Microbiology, Chinese Academy of Sciences
NO.1 West Beichen Road
Chaoyang District
Beijing 100101
P. R. China

[MUMmer-users] MUMmer 3.20 released

[Adam P. <aph...@gm...>]

Hello!
MUMmer 3.20 was released today. A number of build issues, pertaining to the
newer releases of Linux, have been fixed. Also, two new programs were added:
'dnadiff', and 'show-diff'. 'show-diff' is a beta-stage program that
attempts to quantify the number of large-scale differences between two
sequences (inversions, translocations, ...) based on 'nucmer' output.
'dnadiff' is a comparative analysis script that runs 'nucmer', along with
its utilities (including 'show-diff'), and summarizes the results in a
report file. This program is especially well suited for comparing two
assemblies of the same, or nearly identical, organism. See the 'README' and
'doc/dnadiff.README' for more information.

Best regards,
Adam Phillippy

University of Maryland
Center for Bioinformatics and Computational Biology

[MUMmer-users] MUMmer3.18 release

[Adam P. <ada...@ya...>]

Hi All,
A few bugs were identified with the "delta-filter"
utility released with v3.17, so a new version has been
cut to fix these problems. The first was a small
instability problem, and the other caused delta-filter
to  favor simply the longest match instead of the
longest and highest identity match. v3.18 fixes both
of these bugs. You only need to update MUMmer if you
actively use the "delta-filter" utility.

Email the mum...@li... list with
any questions.

Best,
-Adam

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
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[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.
=20
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.
=20
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:
=20
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)
=20
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:
=20
http://www.sourceforge.net/projects/mummer/lists
=20
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.
=20
http://lists.sourceforge.net/lists/listinfo/mummer-devel
http://lists.sourceforge.net/lists/listinfo/mummer-help
http://lists.sourceforge.net/lists/listinfo/mummer-users
=20
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:
=20
http://www.cbcb.umd.edu
=20
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:
=20
http://amos.sourceforge.net
=20
which is also a SourceForge.net project. Browse around or sign up for =
the appropriate mailing lists if you are interested in more information.
=20
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...>
=20
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

=20
--=3D=3D-- MUMMER 3.17 RELEASE NOTES --=3D=3D--
=20
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.
=20
__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
=20
__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
=20
__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
=20
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.

[MUMmer-users] MUMmer-users list is now active

[Adam P. <ada...@ya...>]

The maiden message...


		
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