%0 Journal Article
%T A reference guide for tree analysis and visualization
%A Georgios A Pavlopoulos
%A Theodoros G Soldatos
%A Adriano Barbosa-Silva
%A Reinhard Schneider
%J BioData Mining
%D 2010
%I BioMed Central
%R 10.1186/1756-0381-3-1
%X Tree data structures and representations are essential in biological studies. They are able to show hierarchical organizations of biological data and concepts; for example, some of the most well known efforts for hierarchical representations are the Gene Ontology (GO) [1] that describes the functional annotation of genes via a hierarchically organized set of terms and phrases and the Unified Medical Language System (UMLS) [2] that has a biomedical focus as discussed later. A prime example of tree representations is the so-called tree of life [3] which displays evolutionary relationships between species and how they separated and evolved over time. Tree representations are also valuable for classification and clustering visualization of biological data.Evolutionary studies were always a very important field of biological research. Currently, the modern sequencing techniques and their improvements make it easy to sequence and analyze more and more species. There are approximately 1.7 million identified species, which is just a fraction of the total number of species that exist. Only about 80,000 of these species have been analyzed for evolutionary relationships and have been assigned into a hierarchy [4]. The major challenge remains: the creation of the biggest possible phylogenetic tree of life that will classify all species showing their detailed evolutionary relationships. Ideally, all of the species recognized thus far should have a place in that phylogenetic tree. Therefore, proper visualization tools that will be able to display very wide and deep hierarchies are necessary.Chip-Chip arrays, microarrays, and other proteomics or trascriptomics technologies improve every day and the data produced by them often require statistical and clustering analysis [5], the results of which are usually visualized by tree hierarchies. Nevertheless, methods that greatly simplify the analysis and interpretation of biological data are not enough. Well-designed visualization applic
%U http://www.biodatamining.org/content/3/1/1