Well-designed visualization applications that are developed, eventually transform raw data into logically structured and visually tangible representations. Nevertheless, methods that greatly simplify the analysis and interpretation of biological data are not enough. Therefore, proper visualization tools that will be able to display very wide and deep hierarchies are necessary.Ĭhip-Chip arrays, microarrays, and other proteomics or trascriptomics technologies improve every day and the data produced by them often require statistical and clustering analysis, the results of which are usually visualized by tree hierarchies. Ideally, all of the species recognized thus far should have a place in that phylogenetic tree. The major challenge remains: the creation of the biggest possible phylogenetic tree of life that will classify all species showing their detailed evolutionary relationships. Only about 80,000 of these species have been analyzed for evolutionary relationships and have been assigned into a hierarchy. There are approximately 1.7 million identified species, which is just a fraction of the total number of species that exist. Currently, the modern sequencing techniques and their improvements make it easy to sequence and analyze more and more species. Tree representations are also valuable for classification and clustering visualization of biological data.Įvolutionary studies were always a very important field of biological research. A prime example of tree representations is the so-called tree of life which displays evolutionary relationships between species and how they separated and evolved over time. 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) that describes the functional annotation of genes via a hierarchically organized set of terms and phrases and the Unified Medical Language System (UMLS) that has a biomedical focus as discussed later. Tree data structures and representations are essential in biological studies.
#Geneious free trial software
Here we focus on freely available software that offers to the users various tree-representation methodologies for biological data analysis. We also discuss on how these tools can be developed further and should become integrated with various data sources. We describe the uniform and standard computer readable formats to represent tree hierarchies and we comment on the functionality and the limitations of these tools. In this study, we review tools that are currently available for the visualization of biological trees and analysis, mainly developed during the last decade. For example, the current phylogenetic tree visualization tools are not able to display easy to understand large scale trees with more than a few thousand nodes. Most of the available visualization tools that are able to represent such hierarchies, project data in 2D and are lacking often the necessary user friendliness and interactivity. Clustering analysis is becoming more and more difficult to be applied on very large amounts of data since the results of these algorithms cannot be efficiently visualized. Databases holding information about how data are related and how they are hierarchically organized expand rapidly. Sequencing technologies become cheaper and easier to use and, thus, large-scale evolutionary studies towards the origins of life for all species and their evolution becomes more and more challenging.
The quantities of data obtained by the new high-throughput technologies, such as microarrays or ChIP-Chip arrays, and the large-scale OMICS-approaches, such as genomics, proteomics and transcriptomics, are becoming vast.