NAME
maketree - perform Quartet Tree Reconstruction on a distance matrix to
produce a binary tree
SYNOPSIS
maketree [-n] [-o filename] distmatrix.clb
DESCRIPTION
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 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. 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
http://www.arxiv.org/abs/cs.SD/0303025
OPTIONS
-o filename, --output=FILE
change the default output filename to something other than
treefile.dot
-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.
ENVIRONMENT
none
DIAGNOSTICS
If any of the files cannot be read, an error will be printed and the
program exits with a nonzero exit code.
SEE ALSO
complearn(5), ncd(1)