BaCoCa - A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions
BaCoCa - A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions
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DOI：
10.1016/j.ympev.2013.09.011
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发表时间：
2014-01-01
影响因子：
4.1
通讯作者：
Struck, Torsten H.
中科院分区：
文献类型：
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作者：
Kueck, Patrick;Struck, Torsten H.
BaCoCa (BAse COmposition CAlculator) 是一款用户友好的软件，它结合了多种统计方法（如 RCFV 和 C 值计算）来识别比对序列数据中可能误导系统发育重建的偏差。由于其速度和灵活性，该程序提供了在一次进程运行中分析数百个预定义基因分区和分类单元子集的可能性。 BaCoCa 是命令行驱动的，可以轻松集成到系统基因组研究的自动处理流程中。此外，鉴于制表符分隔的输出样式，结果可以轻松地用于在 Excel 等程序或 R 等统计包中进行进一步分析。BaCoCa 的一个内置选项是使用 R 生成具有某些结果的分层聚类的热图。作为输入文件，BaCoCa 可以处理 FASTA 和宽松的 PHYLIP，这些文件通常用于系统发育管道。 BaCoCa 用 Perl 实现，可在 Windows PC、Mac 和 Linux 操作系统上运行。 BaCoCa 的可执行源代码、示例测试文件和详细文档可在 http://software.zfmk.de 上免费获取。 (C) 2013 Elsevier Inc. 保留所有权利。
BaCoCa (BAse COmposition CAlculator) is a user-friendly software that combines multiple statistical approaches (like RCFV and C value calculations) to identify biases in aligned sequence data which potentially mislead phylogenetic reconstructions. As a result of its speed and flexibility, the program provides the possibility to analyze hundreds of pre-defined gene partitions and taxon subsets in one single process run. BaCoCa is command-line driven and can be easily integrated into automatic process pipelines of phylogenomic studies. Moreover, given the tab-delimited output style the results can be easily used for further analyses in programs like Excel or statistical packages like R. A built-in option of BaCoCa is the generation of heat maps with hierarchical clustering of certain results using R. As input files BaCoCa can handle FASTA and relaxed PHYLIP, which are commonly used in phylogenomic pipelines. BaCoCa is implemented in Perl and works on Windows PCs, Macs and Linux operating systems. The executable source code as well as example test files and a detailed documentation of BaCoCa are freely available at http://software.zfmk.de. (C) 2013 Elsevier Inc. All rights reserved.