NAME

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

DESCRIPTION

       ERROR: Please specify a file containing bootstrap trees via -i.

       This is RogueNaRok version 1.0 released by Andre J. Aberer in 2011-10-25.

       This program implements the RogueNaRok algorithm for rogue taxon identification.

       SYNTAX: RogueNaRok -i <bootTrees> -n <runId> [-x <excludeFile>] [-c <threshold>] [-b]  [-s
       <dropsetSize>] [-w <workingDir>] [-h]

              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.

       -T <num>

              Execute  RogueNaRok in parallel with <num> threads. You need to compile the program
              for parallel execution first.

       -h

              This help file.

       MINIMAL EXAMPLE: ./RogueNaRok -i <bootstrapTreeFile> -n run1

AUTHOR

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