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raxmlGUI: a graphical front-end for RAxML

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Abstract

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/.

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References

  • Blair, C., & Murphy, R. W. (2011). Recent trends in molecular phylogenetic analysis: where to next? Journal of Heredity, 102, 130–138.

    Article  PubMed  Google Scholar 

  • Guindon, S., Duyfayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59, 307–321.

    Article  PubMed  CAS  Google Scholar 

  • Ott, M., & Stamatakis, A. (2010). Preparing RAxML for the SPEC MPI Benchmark Suite. In S. Wagner, M. Steinmetz, A. Bode, & M. M. Müller (Eds.), High Performance Computing in Science and Engineering, Garching/Munich 2009, Part 8 (pp. 757–768). Berlin: Springer.

    Chapter  Google Scholar 

  • 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

  • Pattengale, N. D., Alipour, M., Bininda-Emonds, O. R. P., Moret, B. M. E., & Stamatakis, A. (2010). How many bootstrap replicates are necessary? Journal of Computational Biology, 17, 337–354.

    Article  PubMed  CAS  Google Scholar 

  • Robinson, D. R., & Foulds, L. R. (1981). Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131–147.

    Article  Google Scholar 

  • Shimodaira, H. (2001). Multiple comparisons of log-likelihoods and combining nonnested models with applications to phylogenetic tree selection. Communications in Statistics - Theory and Methods, 30, 1751–1772.

    Article  Google Scholar 

  • Stamatakis, A. (2006a). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688–2690.

    Article  PubMed  CAS  Google Scholar 

  • 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.

  • 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.

  • Stamatakis, A., Blagojevic, F., Nikolopoulos, D. S., & Antonopoulos, C. D. (2007). Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell. Journal of VLSI Signal Processing, 48, 271–286. doi:10.1007/s11265-007-0067-4

    Google Scholar 

  • Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology, 57, 758–771.

    Article  PubMed  Google Scholar 

  • Yang, Z. (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39, 306–314.

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

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.

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Authors and Affiliations

  1. Department of Botany and Molecular Evolution, Research Institute Senckenberg, Senckenberganlage 25, 60325, Frankfurt am Main, Germany

    Daniele Silvestro & Ingo Michalak

  2. Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany

    Daniele Silvestro & Ingo Michalak

  3. Department of Diversity and Evolution of Higher Plants, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany

    Daniele Silvestro & Ingo Michalak

Authors
  1. Daniele Silvestro
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  2. Ingo Michalak
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Correspondence to Daniele Silvestro or Ingo Michalak.

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Daniele Silvestro and Ingo Michalak contributed equally

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Silvestro, D., Michalak, I. raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 12, 335–337 (2012). https://doi.org/10.1007/s13127-011-0056-0

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