Example 3 of the Super3GL program usage

The set of input trees in Example 3 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. This example is similar to Example 2, but it does not use the input trees 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 128 processors in MVAPICH-1.2 environment:

  mpirun -np 128 -maxtime 30 super3GL

  Execution time on the supercomputer MVS-100K in the JSCC RAS is 17 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 3 files: example276.zip.