raxmlGUI: a graphical front-end for RAxML
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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/.
KeywordsRapid bootstrap Graphical user interface Maximum likelihood Phylogenetic analyses Python RAxML
We are grateful to Alexandros Stamatakis, for support and suggestions. Furthermore, we thank Gaëlle Bocksberger, Fernando Fernandez, Rafael Louzada, and Jan Schnitzler for beta-testing and aid. This study was supported financially by the German Research Foundation (DFG, projects ZI 557/6-2, ZI 557/7-1, SCHU 2426/1-1, SCHU 2426/2-2), and the research funding programme “LOEWE Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz” of Hesse’s Ministry of Higher Education, Research, and the Arts.
The authors declare that they have no conflict of interest.
- Pattengale, N. D., Aberer, A. J., Swenson, K. M., Stamatakis, A., & Moret, B. M. E. (2011). Uncovering hidden phylogenetic consensus in large datasets. IEEE/ACM transactions on computational biology and bioinformatics, 03 Feb. 2011. IEEE computer Society Digital Library. IEEE Computer Society, http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.28
- Stamatakis, A. (2006b). Phylogenetic models of rate heterogeneity: A high performance computing perspective. In: Proceedings of the 20th IEEE International Parallel & Distributed Processing Symposium (IPDPS2006), (pp. 278–286). Washington: IEEE Computer Society Press.Google Scholar
- Stamatakis, A. (2008). The RAxML 7.0.4 manual. http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.4.php. Accessed 8 December 2010.
- Stamatakis, A., & Alachiotis, N. (2010). Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinformatics, 26, ISMB 2010, i132–i139.Google Scholar