Example 4 of the Super3GL
program usage
The set of input trees in Example 4 consists of 1511 gene trees (file
all_trees.tre
) for 820 Bacteria species. A leaf label in the gene tree contains
abbreviated species name as the first segment (i.e., before underscore sign). Consequent
segments of the label are the genome number and gene name. The table of full species name
is given in the file BacNames.csv
. Six of 820 species in the table do not occur
in the input trees, and two trees represent only one species. The program removes this spurious
data. Thus, 1509 trees with 814 species remain.
- The program configuration file for running in normal mode (both Stages 1 and 2) is
super3GL.ini
. - Command line to run the program on 512 processors in MVAPICH-1.2 environment:
Execution time on the supercomputer MVS-100K in the JSCC RAS is 391 min.mpirun -np 512 -maxtime 600 super3GL
- The file of basis trees obtained after Stage 1 is
basis.tre
. - The supertree file obtained after Stage 2 is
super3.tre
.Note that the tree is incomplete: 82 of 814 species could not be inserted unambiguously and were skipped (see the end of execution log). - The same file after decoding of abbreviated species names with
uncode
utility:super3n.tre
; it is obtained by the command line:uncode super3.tre BacNames.csv super3n.tre
- The execution log file is
super3GL.log
.
Download the bunch of Example 4 files: example814.zip.