Methods and Applications

Organisms Diversity & Evolution

, Volume 12, Issue 4, pp 335-337

First online:

raxmlGUI: a graphical front-end for RAxML

  • Daniele SilvestroAffiliated withDepartment of Botany and Molecular Evolution, Research Institute SenckenbergBiodiversity and Climate Research Centre (BiK-F)Department of Diversity and Evolution of Higher Plants, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt Email author 
  • , Ingo MichalakAffiliated withDepartment of Botany and Molecular Evolution, Research Institute SenckenbergBiodiversity and Climate Research Centre (BiK-F)Department of Diversity and Evolution of Higher Plants, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt Email author 

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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/​.

Keywords

Rapid bootstrap Graphical user interface Maximum likelihood Phylogenetic analyses Python RAxML