"rio" work
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Thu, 6 Dec 2012 01:46:46 +0000 (01:46 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Thu, 6 Dec 2012 01:46:46 +0000 (01:46 +0000)
commit9f71fc09f5c47e3c68e204a0fc84f95c08d3a892
tree9b9623347d568c1c0dda08f82f6f26c0b5147f86
parenta6111a2153dc12fa437897cafd7e22d85962bc64
"rio" work
315 files changed:
forester/archive/RIO/others/hmmer/00README [deleted file]
forester/archive/RIO/others/hmmer/COPYRIGHT [deleted file]
forester/archive/RIO/others/hmmer/INSTALL [deleted file]
forester/archive/RIO/others/hmmer/LICENSE [deleted file]
forester/archive/RIO/others/hmmer/Makefile.in [deleted file]
forester/archive/RIO/others/hmmer/NOTES [deleted file]
forester/archive/RIO/others/hmmer/Userguide.pdf [deleted file]
forester/archive/RIO/others/hmmer/config.guess [deleted file]
forester/archive/RIO/others/hmmer/config.sub [deleted file]
forester/archive/RIO/others/hmmer/configure [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmalign.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmbuild.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmcalibrate.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmconvert.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmemit.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmer.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmfetch.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmindex.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmpfam.man [deleted file]
forester/archive/RIO/others/hmmer/documentation/man/hmmsearch.man [deleted file]
forester/archive/RIO/others/hmmer/install-sh [deleted file]
forester/archive/RIO/others/hmmer/squid/00README [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/abstract.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/formats.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/gsi-format.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/intro.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/main.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/selex.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/squid-format.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Docs/ssi-format.tex [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/a2m [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/clustal [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/embl [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/fasta [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/formattest.pl [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/gcg [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/gcgdata.1 [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/gcgdata.2 [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/genbank [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/msf [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/phylip [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/pir [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/regression.dat [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/selex.1 [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/selex.2 [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/stockholm.1 [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/stockholm.2 [deleted file]
forester/archive/RIO/others/hmmer/squid/Formats/swissprot [deleted file]
forester/archive/RIO/others/hmmer/squid/INSTALL [deleted file]
forester/archive/RIO/others/hmmer/squid/Makefile.in [deleted file]
forester/archive/RIO/others/hmmer/squid/Man/afetch.man [deleted file]
forester/archive/RIO/others/hmmer/squid/Man/alistat.man [deleted file]
forester/archive/RIO/others/hmmer/squid/Man/seqstat.man [deleted file]
forester/archive/RIO/others/hmmer/squid/Man/sfetch.man [deleted file]
forester/archive/RIO/others/hmmer/squid/Man/shuffle.man [deleted file]
forester/archive/RIO/others/hmmer/squid/Man/sreformat.man [deleted file]
forester/archive/RIO/others/hmmer/squid/a2m.c [deleted file]
forester/archive/RIO/others/hmmer/squid/afetch_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/aligneval.c [deleted file]
forester/archive/RIO/others/hmmer/squid/alignio.c [deleted file]
forester/archive/RIO/others/hmmer/squid/alistat_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/clustal.c [deleted file]
forester/archive/RIO/others/hmmer/squid/cluster.c [deleted file]
forester/archive/RIO/others/hmmer/squid/compalign_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/compstruct_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/configure [deleted file]
forester/archive/RIO/others/hmmer/squid/dayhoff.c [deleted file]
forester/archive/RIO/others/hmmer/squid/eps.c [deleted file]
forester/archive/RIO/others/hmmer/squid/file.c [deleted file]
forester/archive/RIO/others/hmmer/squid/getopt.c [deleted file]
forester/archive/RIO/others/hmmer/squid/gki.c [deleted file]
forester/archive/RIO/others/hmmer/squid/gki.h [deleted file]
forester/archive/RIO/others/hmmer/squid/gsi.c [deleted file]
forester/archive/RIO/others/hmmer/squid/gsi.h [deleted file]
forester/archive/RIO/others/hmmer/squid/gsi64.c [deleted file]
forester/archive/RIO/others/hmmer/squid/gsi64.h [deleted file]
forester/archive/RIO/others/hmmer/squid/hsregex.c [deleted file]
forester/archive/RIO/others/hmmer/squid/install-sh [deleted file]
forester/archive/RIO/others/hmmer/squid/iupac.c [deleted file]
forester/archive/RIO/others/hmmer/squid/msa.c [deleted file]
forester/archive/RIO/others/hmmer/squid/msa.h [deleted file]
forester/archive/RIO/others/hmmer/squid/msf.c [deleted file]
forester/archive/RIO/others/hmmer/squid/phylip.c [deleted file]
forester/archive/RIO/others/hmmer/squid/revcomp.c [deleted file]
forester/archive/RIO/others/hmmer/squid/revcomp_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/rk.c [deleted file]
forester/archive/RIO/others/hmmer/squid/rk.h [deleted file]
forester/archive/RIO/others/hmmer/squid/selex.c [deleted file]
forester/archive/RIO/others/hmmer/squid/seqencode.c [deleted file]
forester/archive/RIO/others/hmmer/squid/seqsplit_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/seqstat_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sfetch_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/shuffle.c [deleted file]
forester/archive/RIO/others/hmmer/squid/shuffle_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sindex_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sqerror.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sqfuncs.h [deleted file]
forester/archive/RIO/others/hmmer/squid/sqio.c [deleted file]
forester/archive/RIO/others/hmmer/squid/squid.h.in [deleted file]
forester/archive/RIO/others/hmmer/squid/squidconf.h.in [deleted file]
forester/archive/RIO/others/hmmer/squid/squidcore.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sre_ctype.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sre_math.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sre_string.c [deleted file]
forester/archive/RIO/others/hmmer/squid/sreformat_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/ssi.c [deleted file]
forester/archive/RIO/others/hmmer/squid/ssi.h [deleted file]
forester/archive/RIO/others/hmmer/squid/stack.c [deleted file]
forester/archive/RIO/others/hmmer/squid/stockholm.c [deleted file]
forester/archive/RIO/others/hmmer/squid/stockholm.h [deleted file]
forester/archive/RIO/others/hmmer/squid/stopwatch.c [deleted file]
forester/archive/RIO/others/hmmer/squid/stopwatch.h [deleted file]
forester/archive/RIO/others/hmmer/squid/test_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/translate.c [deleted file]
forester/archive/RIO/others/hmmer/squid/translate_main.c [deleted file]
forester/archive/RIO/others/hmmer/squid/types.c [deleted file]
forester/archive/RIO/others/hmmer/squid/weight.c [deleted file]
forester/archive/RIO/others/hmmer/squid/weight_main.c [deleted file]
forester/archive/RIO/others/hmmer/src/Makefile.in [deleted file]
forester/archive/RIO/others/hmmer/src/alphabet.c [deleted file]
forester/archive/RIO/others/hmmer/src/camJul97.c [deleted file]
forester/archive/RIO/others/hmmer/src/config.h [deleted file]
forester/archive/RIO/others/hmmer/src/core_algorithms.c [deleted file]
forester/archive/RIO/others/hmmer/src/debug.c [deleted file]
forester/archive/RIO/others/hmmer/src/display.c [deleted file]
forester/archive/RIO/others/hmmer/src/emit.c [deleted file]
forester/archive/RIO/others/hmmer/src/emulation.c [deleted file]
forester/archive/RIO/others/hmmer/src/funcs.h [deleted file]
forester/archive/RIO/others/hmmer/src/globals.h [deleted file]
forester/archive/RIO/others/hmmer/src/histogram.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmalign.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmbuild.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmcalibrate-pvm.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmcalibrate.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmconvert.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmemit.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmfetch.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmindex.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmio.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmpfam-pvm.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmpfam.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmpostal.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmsearch-pvm.c [deleted file]
forester/archive/RIO/others/hmmer/src/hmmsearch.c [deleted file]
forester/archive/RIO/others/hmmer/src/masks.c [deleted file]
forester/archive/RIO/others/hmmer/src/mathsupport.c [deleted file]
forester/archive/RIO/others/hmmer/src/misc.c [deleted file]
forester/archive/RIO/others/hmmer/src/modelmakers.c [deleted file]
forester/archive/RIO/others/hmmer/src/plan7.c [deleted file]
forester/archive/RIO/others/hmmer/src/plan9.c [deleted file]
forester/archive/RIO/others/hmmer/src/postprob.c [deleted file]
forester/archive/RIO/others/hmmer/src/postprob.h [deleted file]
forester/archive/RIO/others/hmmer/src/prior.c [deleted file]
forester/archive/RIO/others/hmmer/src/pvm.c [deleted file]
forester/archive/RIO/others/hmmer/src/states.c [deleted file]
forester/archive/RIO/others/hmmer/src/structs.h [deleted file]
forester/archive/RIO/others/hmmer/src/threads.c [deleted file]
forester/archive/RIO/others/hmmer/src/tophits.c [deleted file]
forester/archive/RIO/others/hmmer/src/trace.c [deleted file]
forester/archive/RIO/others/hmmer/src/weetest.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/Exercises.sh [deleted file]
forester/archive/RIO/others/hmmer/testsuite/Makefile.in [deleted file]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.fa [deleted file]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.nfa [deleted file]
forester/archive/RIO/others/hmmer/testsuite/Optiontests.nslx [deleted file]
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forester/archive/RIO/others/hmmer/testsuite/Optiontests.slx [deleted file]
forester/archive/RIO/others/hmmer/testsuite/README [deleted file]
forester/archive/RIO/others/hmmer/testsuite/alignalign_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/evd_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/fitting_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/fn3-bin [deleted file]
forester/archive/RIO/others/hmmer/testsuite/fn3-bin-swap [deleted file]
forester/archive/RIO/others/hmmer/testsuite/fn3.hmm [deleted file]
forester/archive/RIO/others/hmmer/testsuite/fn3.seed [deleted file]
forester/archive/RIO/others/hmmer/testsuite/masks_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/parsingviterbi_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/titin.fa [deleted file]
forester/archive/RIO/others/hmmer/testsuite/tophits_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/trace_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/trace_test.hmm [deleted file]
forester/archive/RIO/others/hmmer/testsuite/trace_test.seq [deleted file]
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forester/archive/RIO/others/hmmer/testsuite/viterbi_exercise.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/weeviterbi_test.c [deleted file]
forester/archive/RIO/others/hmmer/testsuite/weeviterbi_test.hmm [deleted file]
forester/archive/RIO/others/hmmer/testsuite/weeviterbi_test.seq [deleted file]
forester/archive/RIO/others/hmmer/tutorial/7LES_DROME [deleted file]
forester/archive/RIO/others/hmmer/tutorial/Artemia.fa [deleted file]
forester/archive/RIO/others/hmmer/tutorial/RU1A_HUMAN [deleted file]
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forester/archive/RIO/others/hmmer/tutorial/fn3.slx [deleted file]
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forester/archive/RIO/others/phylip_mod/IMPORTANT_NOTICE [deleted file]
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forester/archive/RIO/others/phylip_mod/src/Makefile [deleted file]
forester/archive/RIO/others/phylip_mod/src/cons.c [deleted file]
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forester/archive/RIO/others/phylip_mod/src/dist.c [deleted file]
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forester/archive/RIO/others/phylip_mod/src/fitch.c [deleted file]
forester/archive/RIO/others/phylip_mod/src/neighbor.c [deleted file]
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forester/archive/RIO/others/phylip_mod/src/proml.c [deleted file]
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forester/archive/RIO/others/puzzle_dqo/ChangeLog [deleted file]
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forester/archive/RIO/others/puzzle_mod/missing [deleted file]
forester/archive/RIO/others/puzzle_mod/mkinstalldirs [deleted file]
forester/archive/RIO/others/puzzle_mod/src/00README [deleted file]
forester/archive/RIO/others/puzzle_mod/src/Makefile [deleted file]
forester/archive/RIO/others/puzzle_mod/src/Makefile.am [deleted file]
forester/archive/RIO/others/puzzle_mod/src/Makefile.in [deleted file]
forester/archive/RIO/others/puzzle_mod/src/README [deleted file]
forester/archive/RIO/others/puzzle_mod/src/gamma.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/gamma.h [deleted file]
forester/archive/RIO/others/puzzle_mod/src/ml.h [deleted file]
forester/archive/RIO/others/puzzle_mod/src/ml1.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/ml2.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/ml3.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/model1.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/model2.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/ppuzzle.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/ppuzzle.h [deleted file]
forester/archive/RIO/others/puzzle_mod/src/puzzle.h [deleted file]
forester/archive/RIO/others/puzzle_mod/src/puzzle1.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/puzzle2.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/sched.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/sched.h [deleted file]
forester/archive/RIO/others/puzzle_mod/src/test [deleted file]
forester/archive/RIO/others/puzzle_mod/src/test.in [deleted file]
forester/archive/RIO/others/puzzle_mod/src/util.c [deleted file]
forester/archive/RIO/others/puzzle_mod/src/util.h [deleted file]