AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses.
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DOI：
10.1186/1471-2105-10-357
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发表时间：
2009-10-28
影响因子：
3
通讯作者：
Shalchian-Tabrizi K
中科院分区：
文献类型：
--
作者：
Kumar S;Skjaeveland A;Orr RJ;Enger P;Ruden T;Mevik BH;Burki F;Botnen A;Shalchian-Tabrizi K
近年来，大型多基因序列比对越来越多地被用于真核生物生命之树的系统基因组重建。这种序列数据的超级矩阵比单基因比对更受青睐，因为它们包含了更多关于古代序列特征的信息，因此更适合解决深度分化的关系。然而，随着比对的扩展，具有误导性系统发育信息的位点数量也在增加。因此，系统基因组分析的一个主要目标是使信息与噪声的比率最大化；这可以通过减少快速进化的位点来实现。
在此，我们介绍一个面向批量处理的基于网络的程序包，名为AIR，它允许：1）将几个单基因转换为一个多基因比对；2）识别多基因比对中的进化速率；3）去除快速进化的位点。这三个过程可以通过AIR - Appender、AIR - Identifier和AIR - Remover（AIR）程序来完成，这些程序可以独立使用，也可以在一个半自动化的流程中使用。AIR生成用户友好的输出文件，其中包含经过过滤和未经过过滤的比对，残基根据其进化速率进行着色。与AIR包相关的其他生物信息学应用可在奥斯陆大学的生物门户网站上获取；这些应用共同极大地提高了系统基因组分析的灵活性、效率和质量。
AIR程序包能够高效地创建多基因比对，并更好地评估序列比对中的进化速率。在最近的几项系统基因组分析中，使用AIR程序去除快速进化的位点提高了系统发育分辨率，并增加了对早期分化真核生物分支模式的统计支持。
Large multigene sequence alignments have over recent years been increasingly employed for phylogenomic reconstruction of the eukaryote tree of life. Such supermatrices of sequence data are preferred over single gene alignments as they contain vastly more information about ancient sequence characteristics, and are thus more suitable for resolving deeply diverging relationships. However, as alignments are expanded, increasingly numbers of sites with misleading phylogenetic information are also added. Therefore, a major goal in phylogenomic analyses is to maximize the ratio of information to noise; this can be achieved by the reduction of fast evolving sites. Here we present a batch-oriented web-based program package, named AIR that allows 1) transformation of several single genes to one multigene alignment, 2) identification of evolutionary rates in multigene alignments and 3) removal of fast evolving sites. These three processes can be done with the programs AIR-Appender, AIR-Identifier, and AIR-Remover (AIR), which can be used independently or in a semi-automated pipeline. AIR produces user-friendly output files with filtered and non-filtered alignments where residues are colored according to their evolutionary rates. Other bioinformatics applications linked to the AIR package are available at the Bioportal , University of Oslo; together these greatly improve the flexibility, efficiency and quality of phylogenomic analyses. The AIR program package allows for efficient creation of multigene alignments and better assessment of evolutionary rates in sequence alignments. Removing fast evolving sites with the AIR programs has been employed in several recent phylogenomic analyses resulting in improved phylogenetic resolution and increased statistical support for branching patterns among the early diverging eukaryotes.
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影响因子：
3.4
作者：
Roure B;Rodriguez-Ezpeleta N;Philippe H
通讯作者：
Philippe H
影响因子：
10.7
作者：
Burki, Fabien;Pawlowski, Jan
通讯作者：
Pawlowski, Jan
影响因子：
3.9
作者：
Dutilh, BE;Huynen, MA;Snel, B
通讯作者：
Snel, B
DOI：
10.1073/pnas.0308602101
发表时间：
2004-05-25
影响因子：
11.1
作者：
Nikolaev, SI;Berney, C;Pawlowski, J
通讯作者：
Pawlowski, J
影响因子：
3.3
作者：
Burki, Fabien;Shalchian-Tabrizi, Kamran;Pawlowski, Jan
通讯作者：
Pawlowski, Jan