Abstract
BackgroundPhylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees.Methodology/Principal FindingsWe introduce TreeVector, a Scalable Vector Graphics–and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print.Conclusions/SignificanceTreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user's own web server. It has already been deployed on two recognized and widely used database Web sites.
Highlights
Producing a graphical visualisation of a phylogenetic tree is a common need of researchers involved in studies of computational biology and molecular evolution
We introduce TreeVector, a Java based phylogenetic visualisation tool which aims to address the diverse and changing needs of the user and take advantage of the standards and technologies which are appropriate to this type of graphical visualisation
Scalable Vector Graphics (SVG) is an XML format for showing twodimensional vector graphics, and is supported natively by the majority of modern web browsers. This format is well suited to online visualisation in phylogenetics, as it can be manipulated and explored in a web browser, produces small files, and can be animated and linked using standard web scripts such as Javascript and CSS (See Figure 1)
Summary
Producing a graphical visualisation of a phylogenetic tree is a common need of researchers involved in studies of computational biology and molecular evolution. The phylogenies produced by these software packages and algorithms are normally saved in a computer readable format for further computational analysis, or human inspection using tree visualisation software. One of the simplest and most common data formats for representation of a tree topology is the Newick [3] parenthesis standard. This format is an effective way of storing information on branch lengths, node names and topology in a compressed and easy to parse format. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees
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