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.

roguenarok-single 1.0.1                           October 2021                              ROGUENAROK-SINGLE(1)