Genetic map visualisation

CMap3D

Genetic linkage mapping enables the study of genome organisation and the association of heritable traits with regions of sequenced genomes. Comparative genetic mapping is particularly powerful as it allows translation of information between related genomes and gives an insight into genome evolution. A common tool for the storage, comparison and visualisation of genetic maps is CMap. However, current visualisation in CMap is limited to the comparison of adjacent aligned maps. To overcome this limitation and in collaboration with CMap developers, we have developed CMap3D, a tool to compare multiple genetic maps in three-dimensional space. CMap3D is based on a client/server model ensuring operability with current CMap data repositories. This tool can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps.

The software is a standalone application written in Processing and Java. Binaries are available for Windows, OSX and Linux, and require Sun Microsystems Java Runtime Environment 1.6 or later. The software is freely available for non-commercial use.

The current version of CMap3D is 0.7 and was released 26/08/2011
show release notes

Changes in 0.7:

• Add link to wheat genome database

Changes in 0.5:

• Fixed a bug where correspondences would not load for features where the feature_acc differed from the feature_id

Changes in (and up to) 0.4:

• Code refactor to make CMap3D compatible with the production version of Processing, v1.0.1
• Added Edwards group maintained Brassica genetic map repository to the master repository list (http://bioinformatics.apcfg.com.au/cmap)
• CMap3D now interacts with the CMap API for CMap versions 1.01 and greater

Download

CMap3D is a stand-alone application and is available for Windows, OS X, and Linux. This software may be downloaded freely for academic use only. For commercial use, please contact David Edwards  to obtain a licence.

We request that users submit their name and email address prior to downloading the software. While this is not compulsory, doing so will provide support for further funding applications and will allow email notification of updates.

Name:
Email address		Include on email list

CMap3D v0.7 for Windows     CMap3D v0.7 for Mac     CMap3D v0.7 for Linux 

Prerequisites

Windows
A current version of Sun Microsystems Java is required. Visit  java.sun.com to get the latest version.

Linux
CMap3D will not work with GNU Java, an installation of Sun Microsystems Java is required*.

Additionally, for full functionality CMap3D is best used in either the Gnome or KDE desktop environments. Other environments have not been tested.

* Some distributions, such as Fedora, implement OpenJDK, Sun Java under an open source license. CMap3D should work with this version of Java but has not been tested. Below are some links to help install Sun Java on your favourite distribution.

CentOS: http://wiki.centos.org/HowTos/JavaOnCentOS
Ubuntu: https://help.ubuntu.com/community/Java

Publications

• Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. Bioinformatics 26 (2) 273-274

• Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27

Links

CMap home

wheat 7DS CMap

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