CAMA


Correspondence analysis on multiple sequence alignments


Roland Schwarz1,2, Philipp Seibel1, Jörg Schultz1 und Tobias Müller1

1Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany

2Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

 roland.schwarz@cancer.org.uk

tobias.mueller@biozentrum.uni-wuerzburg.de




Overview

CAMA is a portable full-featured and open-source software application for co-clustering of sequences and sites in a multiple sequence alignment. It allows for the detection of dependencies between sequences and sites in terms of their chi-square distance and uses a sensible embedding of sequences into a real-valued vector space by exploiting the fisher scores of a Profile Hidden Markov Model.

Current version

The current version is 1.1.0 (April 2010) and can be downloaded via the links from the bottom of the page.

Implementation

CAMA is written purely in Java and runs on Windows, Linux and Mac systems. It is built upon the BioJava framework (http://biojava.org)

CAMA requires the Java Runtime Environment 1.6 (http://java.sun.com/javase/downloads/index.jsp) and relies on the following libraries, which are included in the download archive:

Documentation

For a basic introduction see here. Also have a look at the example files which come with the download. There you will find examples which demonstrate the usage of ordinary (DNA or protein) multiple sequence alignments. Additionally, there are two examples which show the extended use of CAMA for the analysis of arbitrary user-defined sequential datasets (RNA sequence structure alignments and a heapmap dataset).

Licensing

CAMA is distributed under the GNU General Public License (GPL). For more information, see http://www.gnu.org/copyleft/gpl.html or the LICENSE file which comes with the download archive.

References

If you use the software, please cite Schwarz et al. 2009, Nucleic Acids Research

Downloads

CAMA 1.1.0 for Linux, Mac and Windows