NAME

       roguenarok-single  -  implements  the  RogueNaRok algorithm for rogue taxon identification
       (single core version)

SYNOPSIS

       roguenarok-single -i <bootTrees> -n <runId> [-x <excludeFile>] [-c <threshold>]  [-b]  [-s
       <dropsetSize>] [-w <workingDir>] [-h]

OPTIONS

   OBLIGATORY
       -i <bootTrees>
              A collection of bootstrap trees.

       -n <runId>
              An identifier for this run.

   OPTIONAL
       -t <bestKnownTree>
              If  a  single  best-known  tree  (such as an ML or MP tree) is provided, RogueNaRok
              optimizes the bootstrap support in this  best-known  tree  (still  drawn  from  the
              bootstrap trees). The threshold parameter is ignored.

       -x <excludeFile>
              taxa in this file (one taxon per line) will not be considered for pruning.

       -c <threshold>
              A  threshold  or  mode  for  the  consensus tree that is optimized. Specify a value
              between 50 (majority rule consensus) and 100 (strict  consensus)  or  MR  (for  the
              extended  majority rule consensus). Note that rogue taxa identified with respect to
              different thresholds can vary substantially. DEFAULT: MR consensus

       -b     Instead of trying to maximize the support in the  consensus  tree,  the  RogueNaRok
              will  try  to maximize the number of bipartition in the final tree by pruning taxa.
              DEFAULT: off

       -L <factor>
              a weight factor to penalize for dropset size.  Factor=1 is Pattengale's  criterion.
              The  higher  the  value,  the  more  conservative the algorithm is in pruning taxa.
              DEFAULT: 0.0 (=RBIC)

       -s <dropsetSize>
              maximum size of dropset per iteration. If dropsetSize == n,  then  RogueNaRok  will
              test  in  each  iteration  which tuple of n taxa increases optimality criterion the
              most and prunes taxa accordingly. This  improves  the  result,  but  runtimes  will
              increase at least linearly. DEFAULT: 1

       -w <workDir>
              A working directory where output files are created.

       -h     This help file.

EXAMPLES

              roguenarok-single -i <bootstrapTreeFile> -n run1

AUTHOR

       RogueNaRok was released by Andre J. Aberer in 2011-10-25.

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.