raxmlGUI: a graphical front-end for RAxML
raxmlGUI: a graphical front-end for RAxML
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DOI：
10.1007/s13127-011-0056-0
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发表时间：
2012-12-01
影响因子：
1.6
通讯作者：
Michalak, Ingo
中科院分区：
文献类型：
--
作者：
Silvestro, Daniele;Michalak, Ingo
随着分子数据的不断增加，极大似然方法在系统发育重建中获得了新的核心作用。非常快速的树搜索算法已经被开发出来，可以在合理的时间内处理足够大的数据集。近年来，RAxML以其较高的计算性能和准确性在进化生物学家和分类学家中得到了广泛的应用。但是，由于该程序完全基于命令行，因此在可用性方面存在某些缺点。为了克服这个问题，我们开发了raxmlGUI，这是一个图形用户界面，它使RAxML的使用更容易和高度直观，使用户能够执行不同复杂性的系统发育分析。GUI包括RAxML的所有主要选项，并且许多功能是自动化或简化的。此外，一些特性扩展了RAxML的标准用法，比如用自动分区组装连接的对齐。RaxmlGUI是一个开源的Python程序，可以在一个跨平台包中获得，该包集成了用于主要操作系统的RAxML可执行文件。可以从http://sourceforge.net/projects/raxmlgui/下载。
With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated or simplified. In addition, some features extend the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/.