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       maketree  - perform Quartet Tree Reconstruction on a distance matrix to
       produce a binary tree


       maketree [-n] [-o filename] distmatrix.clb


       maketree tries to find an optimal tree to represent an  input  distance
       matrix   matrix.txt.    It   uses   the   Minimum   Cost  Quartet  Tree
       Reconstruction method.  The program starts  with  a  random  tree,  and
       continues  to  try  small  modifications  to  improve  the  tree score.
       Eventually, the tree will stop easily improving.   The  algorithm  will
       write  the  best tree it found to  It will also write all
       "better" trees that it finds along the way to the final tree at the end
       so  that it is safe to stop early with an interrupt.  The output format
       can be Nexus or .dot (Graphviz) format.  The default is graphviz.

       To start maketree you must have a distance matrix  file.   Three  input
       formats  are  supported  for  distance matrixes: text format, complearn
       binary format (.clb), or Nexus format (.nex).   The  filename  for  the
       distance matrix must be given as an argument.

       The following configuration variables are relevant to this command:

       self_agreement_termination: bool
              Whether  or not to insist k number of trees must reach an agreed
              score before the program exits. Default yes.

       max_fail_count: int
              An integer specifying how many  failed  batches  of  trees  must
              occur  in  succession  before the program exits.  Only used when
              self_agreement_termination is off.  Default 100000.

       Input files for this program can be created using the ncd (1)  command.

       For  more  information  on  the  details  of this algorithm, please see
       Algorithmic Clustering of Music by Cilibrasi, Vitanyi, and de  Wolf  at


       -o filename, --output=FILE
              change  the  default  output  filename  to  something other than

       -n, --nexus
              Nexus output format for tree

       FILES  $HOME/.complearn/complearn.conf
              per-user configuration file, overrides systemwide  default;  see
              complearn(5) for further details.




       If  any  of  the files cannot be read, an error will be printed and the
       program exits with a nonzero exit code.


       complearn(5), ncd(1)