maketree - perform Quartet Tree Reconstruction on a distance matrix to produce
a binary tree
maketree [-n] [-o filename]distmatrix.clb
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 treefile.dot. 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
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:
Whether or not to insist k number of trees must reach an agreed score
before the program exits. Default yes.
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.
Input files for this program can be created using the ncd (1) command.