initial commit
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Feb 2011 01:23:45 +0000 (01:23 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Feb 2011 01:23:45 +0000 (01:23 +0000)
commit7f39f89a230adf39809c80c9540c2f5fe33f3b48
tree85c12ba5c8c7c5c3f198672c595333237875ce3a
parent52e0bbbb8c78b6a32eee50855403453f050dce51
initial commit
350 files changed:
forester/archive/RIO/C/Makefile [new file with mode: 0644]
forester/archive/RIO/C/bootstrap_cz.c [new file with mode: 0644]
forester/archive/RIO/COPYRIGHT [new file with mode: 0644]
forester/archive/RIO/IMPORTANT_NOTICE [new file with mode: 0644]
forester/archive/RIO/LICENSE [new file with mode: 0644]
forester/archive/RIO/RIO_INSTALL [new file with mode: 0644]
forester/archive/RIO/data.tar.bz2 [new file with mode: 0644]
forester/archive/RIO/docs/RIO.pdf [new file with mode: 0644]
forester/archive/RIO/others/hmmer/00README [new file with mode: 0644]
forester/archive/RIO/others/hmmer/COPYRIGHT [new file with mode: 0644]
forester/archive/RIO/others/hmmer/INSTALL [new file with mode: 0644]
forester/archive/RIO/others/hmmer/LICENSE [new file with mode: 0644]
forester/archive/RIO/others/hmmer/Makefile.in [new file with mode: 0644]
forester/archive/RIO/others/hmmer/NOTES [new file with mode: 0644]
forester/archive/RIO/others/hmmer/Userguide.pdf [new file with mode: 0644]
forester/archive/RIO/others/hmmer/config.guess [new file with mode: 0755]
forester/archive/RIO/others/hmmer/config.sub [new file with mode: 0755]
forester/archive/RIO/others/hmmer/configure [new file with mode: 0755]
forester/archive/RIO/others/hmmer/documentation/man/hmmalign.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmbuild.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmcalibrate.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmconvert.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmemit.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmer.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmfetch.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmindex.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmpfam.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/documentation/man/hmmsearch.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/install-sh [new file with mode: 0755]
forester/archive/RIO/others/hmmer/squid/00README [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/abstract.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/formats.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/gsi-format.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/intro.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/main.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/selex.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/squid-format.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Docs/ssi-format.tex [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/a2m [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/clustal [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/embl [new file with mode: 0644]
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forester/archive/RIO/others/hmmer/squid/Formats/formattest.pl [new file with mode: 0755]
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forester/archive/RIO/others/hmmer/squid/Formats/gcgdata.1 [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/gcgdata.2 [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/genbank [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/msf [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/phylip [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/pir [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/regression.dat [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/selex.1 [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/selex.2 [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/stockholm.1 [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/stockholm.2 [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Formats/swissprot [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/INSTALL [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Makefile.in [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Man/afetch.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Man/alistat.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Man/seqstat.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Man/sfetch.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Man/shuffle.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/Man/sreformat.man [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/a2m.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/afetch_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/aligneval.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/alignio.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/alistat_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/clustal.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/cluster.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/compalign_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/compstruct_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/configure [new file with mode: 0755]
forester/archive/RIO/others/hmmer/squid/dayhoff.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/eps.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/file.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/getopt.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/gki.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/gki.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/gsi.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/gsi.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/gsi64.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/gsi64.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/hsregex.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/install-sh [new file with mode: 0755]
forester/archive/RIO/others/hmmer/squid/iupac.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/msa.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/msa.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/msf.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/phylip.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/revcomp.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/revcomp_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/rk.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/rk.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/selex.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/seqencode.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/seqsplit_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/seqstat_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sfetch_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/shuffle.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/shuffle_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sindex_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sqerror.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sqfuncs.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sqio.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/squid.h.in [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/squidconf.h.in [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/squidcore.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sre_ctype.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sre_math.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sre_string.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/sreformat_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/ssi.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/ssi.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/stack.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/stockholm.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/stockholm.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/stopwatch.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/stopwatch.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/test_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/translate.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/translate_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/types.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/weight.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/squid/weight_main.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/Makefile.in [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/alphabet.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/camJul97.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/config.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/core_algorithms.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/debug.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/display.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/emit.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/emulation.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/funcs.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/globals.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/histogram.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmalign.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmbuild.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmcalibrate-pvm.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmcalibrate.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmconvert.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmemit.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmfetch.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmindex.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmio.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmpfam-pvm.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmpfam.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmpostal.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmsearch-pvm.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/hmmsearch.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/masks.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/mathsupport.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/misc.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/modelmakers.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/plan7.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/plan9.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/postprob.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/postprob.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/prior.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/pvm.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/states.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/structs.h [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/threads.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/tophits.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/trace.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/src/weetest.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/Exercises.sh [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/Makefile.in [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.fa [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.nfa [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.nslx [new file with mode: 0644]
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forester/archive/RIO/others/hmmer/testsuite/Optiontests.pri [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.slx [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/README [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/alignalign_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/evd_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/fitting_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/fn3-bin [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/fn3-bin-swap [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/fn3.hmm [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/fn3.seed [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/masks_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/parsingviterbi_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/titin.fa [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/tophits_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/trace_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/trace_test.hmm [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/trace_test.seq [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/trace_test.slx [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/viterbi_exercise.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/weeviterbi_test.c [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/weeviterbi_test.hmm [new file with mode: 0644]
forester/archive/RIO/others/hmmer/testsuite/weeviterbi_test.seq [new file with mode: 0644]
forester/archive/RIO/others/hmmer/tutorial/7LES_DROME [new file with mode: 0644]
forester/archive/RIO/others/hmmer/tutorial/Artemia.fa [new file with mode: 0644]
forester/archive/RIO/others/hmmer/tutorial/RU1A_HUMAN [new file with mode: 0644]
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forester/archive/RIO/others/hmmer/tutorial/globins50.msf [new file with mode: 0644]
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forester/archive/RIO/others/phylip_mod/IMPORTANT_NOTICE [new file with mode: 0644]
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forester/archive/RIO/others/phylip_mod/src/fitch.c [new file with mode: 0644]
forester/archive/RIO/others/phylip_mod/src/neighbor.c [new file with mode: 0644]
forester/archive/RIO/others/phylip_mod/src/phylip.c [new file with mode: 0644]
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forester/archive/RIO/others/phylip_mod/src/proml.c [new file with mode: 0644]
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forester/archive/RIO/others/phylip_mod/src/protpars.c [new file with mode: 0644]
forester/archive/RIO/others/phylip_mod/src/seq.c [new file with mode: 0644]
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forester/archive/RIO/others/phylip_mod/src/seqboot.c [new file with mode: 0644]
forester/archive/RIO/others/phylip_mod/src/test_infile_fitch [new file with mode: 0644]
forester/archive/RIO/others/phylip_mod/src/test_infile_protdist [new file with mode: 0644]
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forester/archive/RIO/others/phylip_mod/src/test_infile_protpars [new file with mode: 0644]
forester/archive/RIO/others/phylip_mod/src/test_infile_seqbboot [new file with mode: 0644]
forester/archive/RIO/others/puzzle_dqo/AUTHORS [new file with mode: 0644]
forester/archive/RIO/others/puzzle_dqo/COPYING [new file with mode: 0644]
forester/archive/RIO/others/puzzle_dqo/ChangeLog [new file with mode: 0644]
forester/archive/RIO/others/puzzle_dqo/IMPORTANT_NOTICE [new file with mode: 0644]
forester/archive/RIO/others/puzzle_dqo/INSTALL [new file with mode: 0644]
forester/archive/RIO/others/puzzle_dqo/Makefile [new file with mode: 0644]
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