We present EPoS, a modular software framework for phylogenetic analysis and visualization. Existing phylogenetic software can be split into two groups. Algorithmic packages that provide computational methods for a specific problem, and visualization tools to analyse results. Many algorithmic tools lack in usability, as they are often command line based, while visualizations often suffer from poor graphical user interfaces. EPoS fills this gap by combining a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations and data structures. A consistent interface is used to manage data or to start available computational methods, disconnecting the work flow from the data or applied methods. Currently, EPoS provides algorithms for Distance based Tree reconstruction, tree distances, consensus trees, and supertree methods. All methods are integrated into a pipeline system which allows combinations of methods that are executed sequentially, where the data flow is handled automatically by the system. A comprehensive tree view is included in EPoS. It offers different layouts, colorization, Annotation and export functions and is able to smoothly render trees up to a few thousand leaves. As visualizations are part of the modular system, they can be extended in any direction and new visualization modules can be integrated to handle, Say, phylogenetic networks. To simplify data handling, EPoS allows the user to Create a persistent workspace that contains all used data sets. Data within the workspace are persistently stored in a transparent and extendable backend module.
