FreeView and FreeOView are programs for viewing and optimizing gene expression dendrograms written in Java programming language with Java SDK Standard Edition Version 1.3.
FreeView is a gene expression dendrogram viewer. It supports basic visualization of dendrograms, zooming, color and visualization schemes and image saving in JPG, BMP or PNG formats. FreeOView inherits all the functionality from FreeView, and additionally implements various dendrogram optimization procedures, including local and genetic algorithm-based optimization, and manual optimization with fitness indicator.
Note that for n genes, dendrogram may be displayed in 2^(n-1) ways, so optimization attempts to find a dendrogram that would be optimal according to some global criteria. In its present version (1.0) FreeOView can optimize window-based variance or mutual information function.
The input to both programs is dendrogram of gene expression as created by the program called Cluster by Michael Eisen from UC Berkeley. FreeView can be considered a Java-based implementation of Eisen's TreeView, with some improvements in functionality and (to our experience) stability.
FreeView and FreeOView were developed by Marko Kavcic within his B. Sc. Thesis project under the mentorship of Blaz Zupan.
If you use the programs and publish your results, here is a citation that you should use:
Marko Kavcic, Blaz Zupan: FreeView, http://www.ailab.si, University of Ljubljana, Slovenia, and Baylor College of Medicine, Houston, TX.