GitHub - aberer/RogueNaRok: A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index (original) (raw)

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.