Laboratory of Mathematic methods and models in bioinformatics,
Institute for Information Transmission Problems,
Russian Academy of Sciences

A program for supertree construction

The program is intended for building of the phylogenetic supertree that agrees with a set of known trees as good as possible. In particular, given a set of gene trees, the program builds the tree of species those genes are from. The program implements an original algorithm with a number of enhancements such as parallelization for use on a multiprocessor system supporting MPI (version 1.2 or above). It is noteworthy that the program supports nonbinary (polytomous) source trees.

The program Super3GL is written in C++ and has a command line interface. The code is portable and can be compiled for Windows 32/64-bit, Linux, Unix, MacOS operating systems.

The program Basis3GL implements an alternative algorithm for basis trees building in the case of ill-conditioned input data. This algorithm is significantly slower than one included in Super3GL so it is recommended to run in parallel on a cluster. The program is also written in C++ and has a command line interface.
The basis trees obtained by Basis3GL then may be used to build a supertree with Super3GL and/or Embed3GL programs.

Windows executables (32/64-bit, non-MPI/MPI versions) and the source code for Linux can be freely downloaded from below links. The source code is available free of charge under the GNU General Public License (GPL) version 3.

Downloadable files

Examples of using Super3GL:

• Example with 40 species
• Example with 276 species (pruned with occurrence threshold of 500)
• Example with 276 species (without pruning)
• Example with 814 species
• Example with 91 species for Basis3GL