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Efficient sequence alignment of full genomes

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
Package version:3.22~dfsg-2


mummer for Debian

The program annotate was renamed to mummer-annotate to avoid
name space pollution with libgd-tools.

 -- Andreas Tille <>, Mon, 7 May 2007 14:46:27 +0200


-=- MUMmer3.x README -=-

** NOTE **
A comprehensive HTML user manual is available in the docs/web/manual
subdirectory or at

MUMmer is now an open source package!  Please contact us if you would like
to contribute to the MUMmer project.  For more information or the latest
release please visit the MUMmer homepage at

Please refer t


MUMMER(1)                                                  MUMMER(1)

       mummer - package for sequence alignment of multiple genomes

       mummer-annotate <gapfile><datafile>
       combineMUMs <RefSequence><MatchSequences><GapsFile>
       delta-filter [options]<deltafile>
       dnadiff [options]<reference><query> or [options]-d<deltafile>
       exact-tandems <file><min-ma


mummer (3.22~dfsg-2) unstable; urgency=low

  [ Andreas Tille ]
  * Make sure scripts will use the i


-- Version history --

3.22 - Significant 'dnadiff' bug fixes. Breakpoints, unaligned seqs, and


Machine-readable license summary for MUMmer, see ‘’.

Name    : 

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