12:58:15
Laboratory of Mathematic methods and models in bioinformatics,
Institute for Information Transmission Problems,
Russian Academy of Sciences
Example 3 of the Super3GL program use
Download the bunch of Example 3 files: example276.zip
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 - 17 мин.
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 3 files: example276.zip
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