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 Super3GL
program 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 Basis3GL
program implements an alternative algorithm for basis trees
building in the case of ill-conditioned input data. This algorithm is significantly slower than
the 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 the links below. The source code is available free of charge under the
GNU General Public License (GPL) version 3.
Downloadable files
Version without MPI | Version for MPICH2 1.4.1p | |
---|---|---|
Super3GL executables for Windows 32bit |
1.4.5 | 1.4.5 |
Super3GL executables for Windows 64bit |
1.4.5 | 1.4.5 |
Super3GL user's manual (PDF) |
super3gl_en | |
Super3GL source code for Linux - GNU GPL V3 |
1.4.5 | |
Utility to decode abbreviations in a species tree | uncode | |
Script to root trees | hogfilter3 | |
Basis3GL executables for Windows 32bit |
2.3.2 | 2.3.2 |
Basis3GL executables for Windows 64bit |
2.3.2 | 2.3.2 |
Basis3GL source code for Linux - GNU GPL V3 |
2.3.2 |
Examples of Super3GL
usage
- 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