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RogueNaRok is an algorithm for the identification of rogue taxa in a tree set. How do I install it? Download the code and run the "make" command. For a parallel version of the RogueNaRok algorithm, use "make mode=parallel". Note that, the parallel version requires the pthreads-library. Running one of the programs without arguments will trigger the help message. Just follow the instructions. More info is available on https://github.com/aberer/RogueNaRok/wiki/RogueNaRok . Also, use this site for reporting bugs or ask questions of how to employ RogueNaRok. QUICK START: Have a look in the "example"-directory. For calling RogueNaRok, simply execute ./RogueNaRok -i example/150.bs -n id in the command line. Searching for rogues based on bootstrap values drawn onto a ML tree (from a bootstrap tree set) is done with ./RogueNaRok -i example/150.bs -t example/150.tre -n id Also notice the script utils/pruneWrapper.sh. It facilitates the process of obtaining pruned trees from the RogueNaRok search. Call without arguments and follow the instructions in the help message. CITATION: If RogueNaRok has been useful for your work, please cite as: * A.J. Aberer, D. Krompass, A. Stamatakis: "Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice", Systematic Biology, in press.