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.