SYNOPSISmaketree [-n] [-o filename] distmatrix.clb
DESCRIPTIONmaketree 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 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.
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 http://www.arxiv.org/abs/cs.SD/0303025
- -o filename, --output=FILE
- change the default output filename to something other than treefile.dot
- -n, --nexus
- Nexus output format for tree
- per-user configuration file, overrides systemwide default; see complearn(5) for further details.