Removing old version of mafft to replace with the new
authorpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Tue, 21 Jun 2011 10:01:52 +0000 (10:01 +0000)
committerpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Tue, 21 Jun 2011 10:01:52 +0000 (10:01 +0000)
commit6e0ce943f09b5ac30f3eb8dc0f20bc75114669ce
tree2280c923e03a3c20ec781e4f55a3ab6393c9a3a6
parent48f0451143441afce738d887b0cde1fb5cdbc02e
Removing old version of mafft to replace with the new

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4285 e3abac25-378b-4346-85de-24260fe3988d
253 files changed:
binaries/src/mafft/binaries/contrafoldwrap [deleted file]
binaries/src/mafft/binaries/countlen [deleted file]
binaries/src/mafft/binaries/disttbfast [deleted file]
binaries/src/mafft/binaries/dndblast [deleted file]
binaries/src/mafft/binaries/dndfast7 [deleted file]
binaries/src/mafft/binaries/dndpre [deleted file]
binaries/src/mafft/binaries/dndpre2 [deleted file]
binaries/src/mafft/binaries/dvtditr [deleted file]
binaries/src/mafft/binaries/f2cl [deleted file]
binaries/src/mafft/binaries/getlag [deleted file]
binaries/src/mafft/binaries/mafft [deleted file]
binaries/src/mafft/binaries/mafft-distance [deleted file]
binaries/src/mafft/binaries/mafft-homologs.1 [deleted file]
binaries/src/mafft/binaries/mafft-profile [deleted file]
binaries/src/mafft/binaries/mafft.1 [deleted file]
binaries/src/mafft/binaries/mccaskillwrap [deleted file]
binaries/src/mafft/binaries/multi2hat3s [deleted file]
binaries/src/mafft/binaries/mxscarnamod [deleted file]
binaries/src/mafft/binaries/pair2hat3s [deleted file]
binaries/src/mafft/binaries/pairash [deleted file]
binaries/src/mafft/binaries/pairlocalalign [deleted file]
binaries/src/mafft/binaries/regtable2seq [deleted file]
binaries/src/mafft/binaries/rnatest [deleted file]
binaries/src/mafft/binaries/score [deleted file]
binaries/src/mafft/binaries/seq2regtable [deleted file]
binaries/src/mafft/binaries/setcore [deleted file]
binaries/src/mafft/binaries/sextet5 [deleted file]
binaries/src/mafft/binaries/splittbfast [deleted file]
binaries/src/mafft/binaries/tbfast [deleted file]
binaries/src/mafft/core/Calignm1.c [deleted file]
binaries/src/mafft/core/DNA.h [deleted file]
binaries/src/mafft/core/Falign.c [deleted file]
binaries/src/mafft/core/Falign_localhom.c [deleted file]
binaries/src/mafft/core/Galign11.c [deleted file]
binaries/src/mafft/core/Galign11.c.org [deleted file]
binaries/src/mafft/core/Halignmm.c [deleted file]
binaries/src/mafft/core/Halignmm.c.better [deleted file]
binaries/src/mafft/core/Halignmm.c.juyo [deleted file]
binaries/src/mafft/core/JTT.c [deleted file]
binaries/src/mafft/core/Lalign11.c [deleted file]
binaries/src/mafft/core/Lalign11.c.fast [deleted file]
binaries/src/mafft/core/Lalignmm.c [deleted file]
binaries/src/mafft/core/MSalign11.c [deleted file]
binaries/src/mafft/core/MSalign11.c.m [deleted file]
binaries/src/mafft/core/MSalignmm.c [deleted file]
binaries/src/mafft/core/MSalignmm.c.algAa [deleted file]
binaries/src/mafft/core/MSalignmm.c.algLargeA [deleted file]
binaries/src/mafft/core/MSalignmm.c.alga [deleted file]
binaries/src/mafft/core/MSalignmm.c.algsmalla [deleted file]
binaries/src/mafft/core/MSalignmm.c.back [deleted file]
binaries/src/mafft/core/MSalignmm.c.bkbk [deleted file]
binaries/src/mafft/core/MSalignmm.c.bug [deleted file]
binaries/src/mafft/core/MSalignmm.c.work [deleted file]
binaries/src/mafft/core/Makefile [deleted file]
binaries/src/mafft/core/Qalignmm.c [deleted file]
binaries/src/mafft/core/Qalignmm.c.better [deleted file]
binaries/src/mafft/core/Qalignmm.c.chukan [deleted file]
binaries/src/mafft/core/Qalignmm.c.er [deleted file]
binaries/src/mafft/core/Ralignmm.c [deleted file]
binaries/src/mafft/core/SAalignmm.c [deleted file]
binaries/src/mafft/core/Salignmm.c [deleted file]
binaries/src/mafft/core/Salignmm.c.060407 [deleted file]
binaries/src/mafft/core/Salignmm.c.double [deleted file]
binaries/src/mafft/core/Salignmm.c.fast [deleted file]
binaries/src/mafft/core/Salignmm.c.float [deleted file]
binaries/src/mafft/core/Salignmm.c.work [deleted file]
binaries/src/mafft/core/blosum.c [deleted file]
binaries/src/mafft/core/blosum.h [deleted file]
binaries/src/mafft/core/changelog [deleted file]
binaries/src/mafft/core/constants.c [deleted file]
binaries/src/mafft/core/contrafoldwrap [deleted file]
binaries/src/mafft/core/contrafoldwrap.c [deleted file]
binaries/src/mafft/core/countlen [deleted file]
binaries/src/mafft/core/countlen.c [deleted file]
binaries/src/mafft/core/defs.c [deleted file]
binaries/src/mafft/core/disttbfast [deleted file]
binaries/src/mafft/core/disttbfast.c [deleted file]
binaries/src/mafft/core/disttbfast_dummy.c [deleted file]
binaries/src/mafft/core/dndblast [deleted file]
binaries/src/mafft/core/dndblast.c [deleted file]
binaries/src/mafft/core/dndfast4.c [deleted file]
binaries/src/mafft/core/dndfast7 [deleted file]
binaries/src/mafft/core/dndfast7.c [deleted file]
binaries/src/mafft/core/dndpre [deleted file]
binaries/src/mafft/core/dndpre.c [deleted file]
binaries/src/mafft/core/dndpre2 [deleted file]
binaries/src/mafft/core/dndpre2.c [deleted file]
binaries/src/mafft/core/dndpre_score.c [deleted file]
binaries/src/mafft/core/dp.h [deleted file]
binaries/src/mafft/core/dummy.c [deleted file]
binaries/src/mafft/core/dvtditr [deleted file]
binaries/src/mafft/core/dvtditr.c [deleted file]
binaries/src/mafft/core/dvtditr2.c [deleted file]
binaries/src/mafft/core/f2cl [deleted file]
binaries/src/mafft/core/f2cl.c [deleted file]
binaries/src/mafft/core/fft.c [deleted file]
binaries/src/mafft/core/fft.h [deleted file]
binaries/src/mafft/core/fft2.c [deleted file]
binaries/src/mafft/core/fft3.c [deleted file]
binaries/src/mafft/core/fftFunctions.c [deleted file]
binaries/src/mafft/core/fft_NC.c [deleted file]
binaries/src/mafft/core/functions.h [deleted file]
binaries/src/mafft/core/galn.c [deleted file]
binaries/src/mafft/core/genGalign11.c [deleted file]
binaries/src/mafft/core/genalign11.c [deleted file]
binaries/src/mafft/core/genalign11.c.err [deleted file]
binaries/src/mafft/core/genalign11.c.fixed [deleted file]
binaries/src/mafft/core/genalign11.c.tobisugi [deleted file]
binaries/src/mafft/core/getlag [deleted file]
binaries/src/mafft/core/getlag.c [deleted file]
binaries/src/mafft/core/io.c [deleted file]
binaries/src/mafft/core/io.c.fast [deleted file]
binaries/src/mafft/core/iteration.c [deleted file]
binaries/src/mafft/core/mafft [deleted file]
binaries/src/mafft/core/mafft-distance [deleted file]
binaries/src/mafft/core/mafft-distance.c [deleted file]
binaries/src/mafft/core/mafft-homologs.1 [deleted file]
binaries/src/mafft/core/mafft-homologs.rb [deleted file]
binaries/src/mafft/core/mafft-homologs.tmpl [deleted file]
binaries/src/mafft/core/mafft-profile [deleted file]
binaries/src/mafft/core/mafft-profile.c [deleted file]
binaries/src/mafft/core/mafft.1 [deleted file]
binaries/src/mafft/core/mafft.bat [deleted file]
binaries/src/mafft/core/mafft.tmpl [deleted file]
binaries/src/mafft/core/mafft.tmpl.backup [deleted file]
binaries/src/mafft/core/mafft.tmpl.subopt [deleted file]
binaries/src/mafft/core/mccaskillwrap [deleted file]
binaries/src/mafft/core/mccaskillwrap.c [deleted file]
binaries/src/mafft/core/memo [deleted file]
binaries/src/mafft/core/miyata.h [deleted file]
binaries/src/mafft/core/miyata5.h [deleted file]
binaries/src/mafft/core/mltaln.h [deleted file]
binaries/src/mafft/core/mltaln.h.save [deleted file]
binaries/src/mafft/core/mltaln9.c [deleted file]
binaries/src/mafft/core/mltaln9.c.er [deleted file]
binaries/src/mafft/core/mtxutl.c [deleted file]
binaries/src/mafft/core/mtxutl.h [deleted file]
binaries/src/mafft/core/multi2hat3s [deleted file]
binaries/src/mafft/core/multi2hat3s.c [deleted file]
binaries/src/mafft/core/newick2mafft.rb [deleted file]
binaries/src/mafft/core/nj.c [deleted file]
binaries/src/mafft/core/output [deleted file]
binaries/src/mafft/core/pair2hat3s [deleted file]
binaries/src/mafft/core/pair2hat3s.c [deleted file]
binaries/src/mafft/core/pairash [deleted file]
binaries/src/mafft/core/pairash.c [deleted file]
binaries/src/mafft/core/pairlara.c [deleted file]
binaries/src/mafft/core/pairlocalalign [deleted file]
binaries/src/mafft/core/pairlocalalign.c [deleted file]
binaries/src/mafft/core/partQalignmm.c [deleted file]
binaries/src/mafft/core/partQalignmm.c.dame [deleted file]
binaries/src/mafft/core/partQalignmm.c.ugoku [deleted file]
binaries/src/mafft/core/partSalignmm.c [deleted file]
binaries/src/mafft/core/partSalignmm.c.comment [deleted file]
binaries/src/mafft/core/pscoffee [deleted file]
binaries/src/mafft/core/pscoffee.tmpl [deleted file]
binaries/src/mafft/core/regtable2seq [deleted file]
binaries/src/mafft/core/regtable2seq.c [deleted file]
binaries/src/mafft/core/rna.c [deleted file]
binaries/src/mafft/core/rnatest [deleted file]
binaries/src/mafft/core/rnatest.c [deleted file]
binaries/src/mafft/core/score [deleted file]
binaries/src/mafft/core/score.c [deleted file]
binaries/src/mafft/core/seq2regtable [deleted file]
binaries/src/mafft/core/seq2regtable.c [deleted file]
binaries/src/mafft/core/setcore [deleted file]
binaries/src/mafft/core/setcore.c [deleted file]
binaries/src/mafft/core/sextet5 [deleted file]
binaries/src/mafft/core/sextet5.c [deleted file]
binaries/src/mafft/core/share.h [deleted file]
binaries/src/mafft/core/splittbfast [deleted file]
binaries/src/mafft/core/splittbfast.c [deleted file]
binaries/src/mafft/core/splittbfast.c.diana [deleted file]
binaries/src/mafft/core/splittbfast.c.equi [deleted file]
binaries/src/mafft/core/splittbfast.c.yugo [deleted file]
binaries/src/mafft/core/suboptalign11.c [deleted file]
binaries/src/mafft/core/tbfast [deleted file]
binaries/src/mafft/core/tbfast.c [deleted file]
binaries/src/mafft/core/tbfast2.c [deleted file]
binaries/src/mafft/core/tbfast3.c [deleted file]
binaries/src/mafft/core/tbfast_inttree.c [deleted file]
binaries/src/mafft/core/tddis.c [deleted file]
binaries/src/mafft/core/tditeration.c [deleted file]
binaries/src/mafft/core/treeOperation.c [deleted file]
binaries/src/mafft/core/univscript.tmpl [deleted file]
binaries/src/mafft/core/x [deleted file]
binaries/src/mafft/extensions/Makefile [deleted file]
binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/BPPMatrix.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/Beta.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/GlobalParameters.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/Globaldp.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/Globaldp.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/Main.cc [deleted file]
binaries/src/mafft/extensions/mxscarna_src/Makefile [deleted file]
binaries/src/mafft/extensions/mxscarna_src/McCaskill.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/McCaskill.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/README [deleted file]
binaries/src/mafft/extensions/mxscarna_src/ScoreType.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/StemCandidate.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/Util.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/config.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/nrutil.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/params-weird [deleted file]
binaries/src/mafft/extensions/mxscarna_src/postProcessings.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/CompareToRef.cc [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Defaults.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Defaults.h_backup [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/EMtrainingALL.txt [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/EvolutionaryTree.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FileBuffer.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FixRef.cc [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Main.cc [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/MakeGnuPlot.cc [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Makefile [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/MultiSequence.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/ProbabilisticModel.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/ProjectPairwise.cc [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/README [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/SafeVector.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/ScoreType.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Sequence.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/SparseMatrix.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/mlparams0 [deleted file]
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/train-script [deleted file]
binaries/src/mafft/extensions/mxscarna_src/scarna.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/seq2scs.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/vienna/COPYING [deleted file]
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_const.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_par.h [deleted file]
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.cpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.hpp [deleted file]
binaries/src/mafft/extensions/mxscarna_src/vienna/params.h [deleted file]
binaries/src/mafft/extensions/mxscarnamod [deleted file]
binaries/src/mafft/extensions/univscript.tmpl [deleted file]
binaries/src/mafft/license [deleted file]
binaries/src/mafft/license.extensions [deleted file]
binaries/src/mafft/readme [deleted file]
binaries/src/mafft/scripts/mafft [deleted file]
binaries/src/mafft/scripts/mafft-homologs.rb [deleted file]
binaries/src/mafft/test/sample [deleted file]
binaries/src/mafft/test/sample.dpparttree [deleted file]
binaries/src/mafft/test/sample.fftns2 [deleted file]
binaries/src/mafft/test/sample.fftnsi [deleted file]
binaries/src/mafft/test/sample.gins1 [deleted file]
binaries/src/mafft/test/sample.ginsi [deleted file]
binaries/src/mafft/test/sample.lins1 [deleted file]
binaries/src/mafft/test/sample.linsi [deleted file]
binaries/src/mafft/test/sample.parttree [deleted file]
binaries/src/mafft/test/samplerna [deleted file]
binaries/src/mafft/test/samplerna.xinsi-globalpair [deleted file]
binaries/src/mafft/test/samplerna.xinsi-scarnapair [deleted file]