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13/12/18
03:19:17

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

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Example 2 of the Super3GL program use

Download the bunch of Example 2 files: example108.zip

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 - 12 min.

The file of basis trees obtained after Stage 1 - basis.tre

The supertree file obtained after Stage 2 - super3.tre

The execution log - super3GL.log

Download the bunch of Example 2 files: example108.zip

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