A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index
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example
utils
Array.c
Array.h
BitVector.c
BitVector.h
Dropset.c
Dropset.h
HashTable.c
HashTable.h
List.c
List.h
Makefile
Node.c
Node.h
ProfileElem.c
ProfileElem.h
README
RogueNaRok.c
Tree.c
Tree.h
common.c
common.h
legacy.c
legacy.h
newFunctions.c
newFunctions.h
parallel.c
parallel.h
rnr-lsi.c
rnr-mast.c
rnr-prune.c
rnr-tii.c
sharedVariables.h

README

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.