Skip to content

A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index

aberer/RogueNaRok

Repository files navigation

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.

About

A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index

Resources

Stars

Watchers

Forks

Packages

No packages published

Languages