Abstract
BackgroundCollaborative tools are of great help in conducting projects involving distant workers. Recent web technologies have helped to build such tools for jointly editing office documents and scientific data, yet none are available for handling phylogenies. Though a large number of studies and projects in evolutionary biology and systematics involve collaborations between scientists of different institutes, current tree comparison visualization software and websites are directed toward single-user access. Moreover, tree comparison functionalities are dispersed between different software that mainly focus on high level single tree visualization but to the detriment of basic tree comparison features.ResultsThe web platform presented here, named CompPhy, intends to fill this gap by allowing collaborative work on phylogenies and by gathering simple advanced tools dedicated to tree comparison. It offers functionalities for tree edition, tree comparison, supertree inference and data management in a collaborative environment. The latter aspect is a specific feature of the platform, allowing people located in different places to work together at the same time on a common project. CompPhy thus proposes shared tree visualization, both synchronous and asynchronous tree manipulation, data exchange/storage, as well as facilities to keep track of the progress of analyses in working sessions. Specific advanced comparison tools are also available, such as consensus and supertree inference, or automated branch swaps of compared trees. As projects can be readily created and shared, CompPhy is also a tool that can be used easily to interact with students in a educational setting, either in the classroom or for assignments.ConclusionsCompPhy is the first web platform devoted to the comparison of phylogenetic trees allowing real-time distant collaboration on a phylogenetic/phylogenomic project. This application can be accessed freely with a recent browser at the following page of the ATGC bioinformatics platform: http://www.atgc-montpellier.fr/compphy/.
Highlights
Collaborative tools are of great help in conducting projects involving distant workers
CompPhy is a web platform devoted to collaborative work on phylogenies, providing facilities to jointly visualize, manipulate and mainly compare trees
Note that it allows a user to see on the screen changes performed by distant collaborators. This is very useful to support a phone or video conversation about a collection of trees tp overcome the need for repeated exchanges of tree files on a shared folder together with round trips with the users’ separate – unsynchronized – tree visualization software
Summary
Trees are the central object handled by CompPhy. They are contained in tree collections, investigated in projects, each of which can be accessed by a declared list of users (possibly by anyone knowing the URL if the project is declared to be public). Zone 2 first displays the project menu and the collaborative box (on the righthand side) enabling users to coordinate their actions when jointly visualizing a project This box allows them to indicate which person is in charge of a current edit. An option enables a user to detach their browser from the activity performed by the others (SYNCHRONIZE tool) In this case, they can change the trees displayed on the workbenches but they can not make any concrete changes in the project, as this would interfere with the actions of the user in control. Subtrees containing taxa present in just one tree are in grey, so that the structure of the consensus tree is clearly apparent This has a main advantage to highlight — inside each of the two compared trees — the topological part on which they agree. The MRP method is implemented via the Spruce library [27] to create the matrix representation of a set
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