CompPhy: a web-based collaborative platform for comparing phylogenies

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/.

[1]  Tim Kovacs,et al.  TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web , 2010, PloS one.

[2]  M. Ragan.  Phylogenetic inference based on matrix representation of trees. , 1992, Molecular phylogenetics and evolution.

[3]  R. Page,et al.  Trees within trees: phylogeny and historical associations. , 1998, Trends in ecology & evolution.

[4]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[5]  B. Baum.  Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees , 1992 .

[6]  Serdar Tasiran,et al.  TreeJuxtaposer: scalable tree comparison using Focus+Context with guaranteed visibility , 2003, ACM Trans. Graph..

[7]  J. Dutheil,et al.  Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs , 2008, BMC Evolutionary Biology.

[8]  William H. Piel,et al.  PhyloWidget: web-based visualizations for the tree of life , 2008, Bioinform..

[9]  Vincent Berry,et al.  ScripTree: scripting phylogenetic graphics , 2010, Bioinform..

[10]  Marie-Christine Brun,et al.  TreeDyn: towards dynamic graphics and annotations for analyses of trees , 2006, BMC Bioinformatics.

[11]  Samuel A. Smits,et al.  jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web , 2010, PloS one.

[12]  Songnian Hu,et al.  EvolView, an online tool for visualizing, annotating and managing phylogenetic trees , 2012, Nucleic Acids Res..

[13]  Michael Kaufmann,et al.  Comparing trees via crossing minimization , 2005, J. Comput. Syst. Sci..

[14]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[15]  Joaquín Dopazo,et al.  ETE: a python Environment for Tree Exploration , 2010, BMC Bioinformatics.

[16]  Christian M. Zmasek,et al.  phyloXML: XML for evolutionary biology and comparative genomics , 2009, BMC Bioinformatics.

[17]  Vincent Berry,et al.  PhySIC_IST: cleaning source trees to infer more informative supertrees , 2008, BMC Bioinformatics.

[18]  Frédéric Delsuc,et al.  PhyloExplorer: a web server to validate, explore and query phylogenetic trees , 2009, BMC Evolutionary Biology.

[19]  Daniel H. Huson,et al.  Dendroscope: An interactive viewer for large phylogenetic trees , 2007, BMC Bioinformatics.

[20]  O. Bininda-Emonds.  Phylogenetic Supertrees: Combining Information To Reveal The Tree Of Life , 2004 .

[21]  Remco R. Bouckaert,et al.  DensiTree: making sense of sets of phylogenetic trees , 2010, Bioinform..

[22]  Andy Purvis,et al.  Getting to the roots of matrix representation. , 2005, Systematic biology.

[23]  Joseph L. Thorley,et al.  RadCon: phylogenetic tree comparison and consensus , 2000, Bioinform..

[24]  G. Moore,et al.  Fitting the gene lineage into its species lineage , 1979 .

[25]  Sebastian Böcker,et al.  EPoS: a modular software framework for phylogenetic analysis , 2008, Bioinform..

[26]  Jeannine Cavender-Bares,et al.  Synthesizing phylogenetic knowledge for ecological research , 2012 .

[27]  Roderic D M Page,et al.  Visualizing Phylogenetic Trees Using TreeView , 2003, Current protocols in bioinformatics.

[28]  M. Charleston,et al.  Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. , 2002, Systematic biology.

[29]  Peer Bork,et al.  Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy , 2011, Nucleic Acids Res..