phyloXML: XML for evolutionary biology and comparative genomics.
phyloXML: XML for evolutionary biology and comparative genomics.
复制标题
DOI：
10.1186/1471-2105-10-356
复制
发表时间：
2009-10-27
影响因子：
3
通讯作者：
Zmasek CM
中科院分区：
文献类型：
--
作者：
Han MV;Zmasek CM
进化树是广泛的生物学研究的核心。在许多这些研究中，树节点和分支需要与各种属性相关联（或注释）。例如，在生物体关系的研究中，树节点与分类学名称相关联，而树枝有长度，通常支持值。在比较基因组学或基因组学中使用的基因树通常用分类信息、基因组相关数据（如基因名称和功能注释）以及事件（如基因复制、物种形成或外显子重排）与进化树本身相关的信息进行注释。目前用于进化树的数据标准具有有限的能力来合并不同数据类型的这种注释。我们开发了一种XML语言，命名为XML，用于描述进化树，以及各种相关的数据项。PhyloXML为常用的项目提供元素，例如分支长度、支持值、分类名称以及基因名称和标识符。通过使用“属性”元素，XML可以适应新的和不可预见的用例。我们还开发了各种用于阅读、写入、转换和可视化XML格式数据的软件工具。PhyloXML是一种由XSD中的完整模式定义的XML语言，它允许存储和交换进化树的结构以及相关数据。有关XMLXML本身、XSD模式以及实现和支持XMLXML的工具的更多信息，请访问。
Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types. We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data. PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at .
登录
查看更多内容
影响因子：
3.3
作者：
Leebens-Mack, Jim;Vision, Todd;Zmasek, Christian
通讯作者：
Zmasek, Christian
影响因子：
5.8
作者：
Zmasek, CM;Eddy, SR
通讯作者：
Eddy, SR
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
TreeViewJ：查看和分析系统发育树的应用程序。
影响因子：
--
作者：
Peterson, Matthew W;Colosimo, Marc E
通讯作者：
Colosimo, Marc E
影响因子：
12.3
作者：
Zmasek CM;Zhang Q;Ye Y;Godzik A
通讯作者：
Godzik A