This page is for the implementation of the method described
in Rooted Triple Consensus and Anomalous Gene Trees, Greg
Ewing, Ingo Ebersberger, Heiko A. Schmidt and Arndt von
The program is called triplec for Triple consensus and is
written in java version 1.5. So it should run without
problems on Mac, Windows and *nix machines. Although the
program has been tested quite thoroughly it is a work in
progress and must be treated as such. In particular most of
the testing and simulations were mainly done on bifurcated
trees. Finally don't forget that this method works only for
Triplec is free to use for commercial and non commercial
purposes but comes with no warranty expressed or implied.
It is provided as is because it may be useful.
The source can be requested and its availability will be
decided on a case by case basis. The reason is that some of
the code has dependencies with a very large code base and
not all of this is relevant to this program and much of this
code is not yet ready for release.
Some time later this year when the rest of the code base has
been properly checked for other dependencies and is ready
for release, this code will be published under one of the
open source licences. Most likely LGPL 2 or a BSD licence.
java -jar Triplec.jar NoReps InFile.newick
Here NoReps is the number of triple reconstructions to use
for the consensus. This is required because reconstruction
is a randomised algorithm. For small trees of about 20 taxa
1000 replicates is enough. But larger numbers should be used
for bigger data sets.
InFile.newick is a text file with one newick tree per
line. The trees are considered to be rooted and each tree
must contain only the taxa labels of the first tree. That is
trees after the first must not contain new taxa.
Although it is not a error to have trees with less taxa than
the first tree as part of the consensus, this method is not
a supertree method. Performance under these conditions has
not been tested and we expect would perform poorly.
Tips, Memory and Performance
This code is not highly optimised as of yet. But this should
not be a big constraint for most people as its performance
and memory requirements are reasonably modest. Remember
that by default java will only give 64 MB to a program and
so on bigger trees it will seem to run out of memory. Just
use the -Xmx switch in java.
Example: java -Xmx500M -jar Triplec.jar 10000
Bugs and Feature requests
Please direct all bug reports and feature request to greg
dot ewing AT univie.ac.at. Please use the subject heading