An Alternative Approach to Multiple Genome Comparison.
Please cite THIS
paper if you use
implements an original approach to multiple genome comparison.
It segments a target genome with respect to its local similarities with k other reference genomes, and classifies its genomic regions according to two criteria:
- being shared or unshared across all genomes,
- offering a unique or several alignment possibilities.
It then intersects the available annotations of the target genome with classified regions and predetermine annotations that can be potentially transfer on the other genomes.
The user can then select among those annotations with respect to their alignment percentage of identity, feature type, etc., complete them with comments, and finally proceed to the transfer by exporting the annotations to a file in a standard format (Sequin/EMBL/GenBank).
is a program equipped with a friendly graphical user interface (GUI).
Source code & Binaries
is distributed under the GPL
-compliant CeCILL license
Qod version 1.0.2 is the latest available release.
wxWidget version 2.8.12 is now requiered (since it fixes lots of bugs
that causes crash when using version 2.8.9).
Adding option '--warn' to activate warnings (they are off by default,
they previously were on by default and where turned off when option
'--quiet' was given.
Now, option '--quiet' discard printing of segmentation and partition.
Order of the options doesn't matter anymore.
You can download the sources of version 1.0.2 and its binaries here
has been demonstrated at the Human Genome Meeting
in Montpellier (18 - 21 May 2010), at the RECOMB Satellite Workshop on Comparative Genomics
in Ottawa (9 - 11 October 2010) and at the Journées Ouvertes en Biologie, Informatique et Mathématiques
in Montpellier (7 - 9 September 2010).
- is fast, flexible, interactive,
- works on multiple OS,
- exploits multi-core computers,
- accepts gzip compressed inputs,
- can process unassembled/unfinished genomes.