CompPhy: a web-based collaborative platform for comparing phylogenies.
CompPhy: a web-based collaborative platform for comparing phylogenies.
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DOI：
10.1186/s12862-014-0253-5
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发表时间：
2014-12-14
影响因子：
3.4
通讯作者：
Chifolleau AM
中科院分区：
文献类型：
--
作者：
Fiorini N;Lefort V;Chevenet F;Berry V;Chifolleau AM
协作工具在执行涉及远程工作人员的项目方面有很大帮助。最近的网络技术帮助建立了这样的工具，用于联合编辑办公室文件和科学数据，但没有一种工具可用于处理系统发育。尽管进化生物学和系统学中的大量研究和项目涉及不同研究所的科学家之间的合作，但目前的树比较可视化软件和网站都是面向单用户访问的。此外，树比较功能分散在不同的软件之间，这些软件主要专注于高级单树可视化，但损害了基本的树比较功能。这里介绍的网络平台，名为CompPhy，打算通过允许在系统发育方面进行协作工作，并通过收集专门用于树木比较的简单高级工具来填补这一空白。它提供了树编辑、树比较、超树推理和协作环境中的数据管理功能。后一方面是该平台的一个具体功能，允许位于不同地点的人们在同一时间一起工作在一个共同的项目上。因此，CompPhy提出了共享树可视化、同步和异步树操作、数据交换/存储以及在工作会话中跟踪分析进度的工具。还提供了特定的高级比较工具，例如共识和超树推理，或比较树的自动分支交换。由于项目可以很容易地创建和共享，CompPhy也是一个可以在教育环境中轻松地与学生互动的工具，无论是在课堂上还是在作业中。CompPhy是第一个致力于系统发育树比较的网络平台，允许在系统发生/系统基因组学项目上进行实时远程协作。该应用程序可以在ATGC生物信息学平台的以下页面使用最新的浏览器免费访问：http://www.atgc-montpellier.fr/compphy/.
Collaborative 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. The 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. CompPhy 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/.
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影响因子：
3.7
作者：
Pethica R;Barker G;Kovacs T;Gough J
通讯作者：
Gough J
影响因子：
4.1
作者：
Ragan, Mark A.
通讯作者：
Ragan, Mark A.
影响因子：
5.8
作者：
Chevenet, Francois;Croce, Olivier;Berry, Vincent
通讯作者：
Berry, Vincent
影响因子：
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作者：
Munzner, T;Guimbretière, F;Zhou, YH
通讯作者：
Zhou, YH
树突镜：大型系统发育树的互动观众。
影响因子：
3
作者：
Huson, Daniel H.;Richter, Daniel C.;Rausch, Christian;Dezulian, Tobias;Franz, Markus;Rupp, Regula
通讯作者：
Rupp, Regula