Example 2 of the Super3GL program usage

The set of input trees in Example 2 consists of 11516 gene trees (file new_trees.tre). These genes are from 276 “species” which are high-level taxa to appear in a sought-for supertree. No table of species is provided. A leaf label in the gene tree contains a name of the taxon as the first segment (i.e., before underscore sign). Consequent segments of the label may be names of a family, strain, macromolecule, gene, etc. In this example, a pruning of the trees is applied: if a high-level taxon rarely occurs in the input trees (below the threshold p=500), such taxon is removed. Thus, 11184 trees with 108 species remain after the pruning.

• The program configuration file for running in normal mode (both Stages 1 and 2) is super3GL.ini.
• Command line to run the program on 32 processors in MPICH2-1.4.1 environment:

  mpirun -np 32 super3GL

  Execution time on the 32-core Xeon 2 GHz Windows-operated server is 12 min.
• The file of basis trees obtained after Stage 1 is basis.tre.
• The supertree file obtained after Stage 2 is super3.tre.
• The execution log file is super3GL.log.

Download the bunch of Example 2 files: example108.zip.