| AITEC Contract Research Projects in FY1996 : software |
At present, we implemented programs for reconstruction of phylogenetic trees in DeepForest. Amino acid data is available. The programs were written based on the maximum likelihood method, in parallel logic programming (KL1/KLIC). The programs should be executed in a parallel environment. We used the Felsenstein (1981) algorithm. On the other hand, we prepared a set of useful predicates for actual data analyses. By using these predicates, users can perform; Generating topologies, Converting data formats, Generating bibliography database, Performing probability calculation, and so on.
In sequential execution, the programs can be executed on most UNIX-based OS with KLIC. We confirmed execution of the programs on; Fujitsu S-4/20L Solaris 2.3/2.4/2.5, Sun SparcStation IPX Sun OS 4.1.2 and, Macintosh Duo 280c MacOS 7.5.1+MachTen 2.2.. In a distributed memory environment, we need both PVM and KLIC. We confirmed execution of the programs on; Fujitsu S-4/20L Solaris 2.3/2.4/2.5. Furthermore, we need a patch included in this software. In a shared memory environment, we confirmed execution of the programs on; Cray CS6400. We need a patch included in this software. The above two patches are courtesy of Dr. T. Chikayama (chikayama@logos.t.u-tokyo.ac.jp).
df.tar.gz comprises the following files (*.kl1: sources, *.com: compile shell scripts, *.doc: documents, others: patches). drwxr-xr-x101/60001 0 May 19 16:30 1997 ./df/ -rw-r--r--101/60001 2090 May 19 16:18 1997 ./df/DeepForest.e.doc drwxr-xr-x101/60001 0 May 19 15:54 1997 ./df/src/ -rw-r--r--101/60001 2234 Jul 30 23:42 1996 ./df/src/print_sequences.kl1 -rwxr-xr-x101/60001 71 Jul 30 23:41 1996 ./df/src/print_sequences.com -rwxr-xr-x101/60001 756 Mar 21 14:13 1997 ./df/src/make_ph drwxr-xr-x101/60001 0 May 19 16:13 1997 ./df/src/patch/ -rw-r--r--101/60001 71647 May 19 16:12 1997 ./df/src/patch/shared.gfloat.sh -rw-r--r--101/60001 9716 Jun 21 12:30 1996 ./df/src/patch/gfloat.c -rw-r--r--101/60001 6817 May 19 15:01 1997 ./df/src/ancestor.kl1 -rw-r--r--101/60001 1998 May 19 15:01 1997 ./df/src/beautify.kl1 -rw-r--r--101/60001 1523 May 19 15:01 1997 ./df/src/consensus.kl1 -rw-r--r--101/60001 12309 May 19 15:01 1997 ./df/src/curvature.kl1 -rw-r--r--101/60001 5130 May 19 15:01 1997 ./df/src/dX.kl1 -rw-r--r--101/60001 1840 May 19 15:01 1997 ./df/src/divide.kl1 -rw-r--r--101/60001 2680 May 19 15:01 1997 ./df/src/dot_matrix.kl1 -rw-r--r--101/60001 1967 May 19 15:01 1997 ./df/src/extract_author.kl1 -rw-r--r--101/60001 4567 May 19 15:01 1997 ./df/src/extract_fields.kl1 -rw-r--r--101/60001 713 May 19 15:01 1997 ./df/src/factorial.kl1 -rw-r--r--101/60001 1436 May 19 15:01 1997 ./df/src/float.kl1 -rw-r--r--101/60001 3087 May 19 15:01 1997 ./df/src/format.kl1 -rw-r--r--101/60001 4646 May 19 15:01 1997 ./df/src/fx.kl1 -rw-r--r--101/60001 11650 May 19 15:01 1997 ./df/src/get_seq.kl1 -rw-r--r--101/60001 472 May 19 15:01 1997 ./df/src/int.kl1 -rw-r--r--101/60001 2636 May 19 15:01 1997 ./df/src/interleave.kl1 -rw-r--r--101/60001 467 May 19 15:01 1997 ./df/src/invert.kl1 -rw-r--r--101/60001 565 May 19 15:01 1997 ./df/src/lines2string.kl1 -rw-r--r--101/60001 3361 May 19 15:01 1997 ./df/src/list.kl1 -rw-r--r--101/60001 6947 May 19 15:01 1997 ./df/src/log_like.kl1 -rw-r--r--101/60001 24531 May 19 15:01 1997 ./df/src/make_bib.kl1 -rw-r--r--101/60001 5672 May 19 15:01 1997 ./df/src/make_destbl.kl1 -rw-r--r--101/60001 9488 May 19 15:01 1997 ./df/src/make_gap_matrix.kl1 -rw-r--r--101/60001 3671 May 19 15:01 1997 ./df/src/make_records.kl1 -rw-r--r--101/60001 10634 May 19 15:01 1997 ./df/src/make_seq.kl1 -rw-r--r--101/60001 2278 May 19 15:01 1997 ./df/src/matrix.kl1 -rw-r--r--101/60001 10519 May 19 15:01 1997 ./df/src/newton.kl1 -rw-r--r--101/60001 11551 May 19 15:01 1997 ./df/src/plot_like.kl1 -rw-r--r--101/60001 2099 May 19 15:01 1997 ./df/src/probability.kl1 -rw-r--r--101/60001 4631 May 19 15:01 1997 ./df/src/remove_gap_site.kl1 -rw-r--r--101/60001 5835 May 19 15:01 1997 ./df/src/search_str.kl1 -rw-r--r--101/60001 6513 May 19 15:01 1997 ./df/src/synonymous.kl1 -rw-r--r--101/60001 3931 May 19 15:01 1997 ./df/src/termio.kl1 -rw-r--r--101/60001 11794 May 19 15:01 1997 ./df/src/tree.kl1 -rw-r--r--101/60001 1951 May 19 15:01 1997 ./df/src/test_tra.kl1 -rw-r--r--101/60001 54768 May 19 15:01 1997 ./df/src/traverse.1.0.kl1 -rw-r--r--101/60001 54956 May 19 15:01 1997 ./df/src/traverse.kl1 -rwxr-xr-x101/60001 40 May 19 15:04 1997 ./df/src/ancestor.com -rwxr-xr-x101/60001 57 May 19 15:04 1997 ./df/src/beautify.com -rwxr-xr-x101/60001 59 May 19 15:04 1997 ./df/src/consensus.com -rwxr-xr-x101/60001 87 May 19 15:04 1997 ./df/src/curvature.com -rwxr-xr-x101/60001 64 May 19 15:04 1997 ./df/src/dot_matrix.com -rwxr-xr-x101/60001 80 May 19 15:04 1997 ./df/src/extract_fields.com -rwxr-xr-x101/60001 69 May 19 15:04 1997 ./df/src/format.com -rwxr-xr-x101/60001 72 May 19 15:04 1997 ./df/src/fx.com -rwxr-xr-x101/60001 72 May 19 15:04 1997 ./df/src/get_seq.com -rwxr-xr-x101/60001 61 May 19 15:04 1997 ./df/src/interleave.com -rwxrwxr-x101/60001 45 May 19 15:04 1997 ./df/src/invert.com -rwxr-xr-x101/60001 65 May 19 15:04 1997 ./df/src/lines2string.com -rwxr-xr-x101/60001 200 May 19 15:04 1997 ./df/src/log_like.com -rwxr-xr-x101/60001 72 May 19 15:04 1997 ./df/src/make_bib.com -rwxr-xr-x101/60001 63 May 19 15:04 1997 ./df/src/make_destbl.com -rwxr-xr-x101/60001 97 May 19 15:05 1997 ./df/src/make_gap_matrix.com -rwxr-xr-x101/60001 51 May 19 15:05 1997 ./df/src/make_records.com -rwxr-xr-x101/60001 83 May 19 15:05 1997 ./df/src/make_seq.com -rwxr-xr-x101/60001 81 May 19 15:05 1997 ./df/src/newton.com -rwxr-xr-x101/60001 87 May 19 15:05 1997 ./df/src/plot_like.com -rwxr-xr-x101/60001 89 May 19 15:05 1997 ./df/src/remove_gap_site.com -rwxr-xr-x101/60001 46 May 19 15:05 1997 ./df/src/synonymous.com -rwxr-xr-x101/60001 209 May 19 15:05 1997 ./df/src/test_tra.1.0.com -rwxr-xr-x101/60001 201 May 19 15:05 1997 ./df/src/test_tra.com -rw-r--r--101/60001 2090 May 19 16:18 1997 ./df/DeepForest.j.doc
www-admin@icot.or.jp