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(parent: 6e0ce94) | patch
new mafft v 6.857 with extensions
authorpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Tue, 21 Jun 2011 10:02:51 +0000 (10:02 +0000)
committerpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Tue, 21 Jun 2011 10:02:51 +0000 (10:02 +0000)
commit063b30bb5e8161134ae764742636ab538e10eea7
tree3bea06b61c7e0b252b8386837fa6f1034432bb7ctree | snapshot
parent6e0ce943f09b5ac30f3eb8dc0f20bc75114669cecommit | diff
new mafft v 6.857 with extensions

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4286 e3abac25-378b-4346-85de-24260fe3988d
158 files changed:
binaries/src/mafft/core/DNA.h [new file with mode: 0644] blob
binaries/src/mafft/core/Falign.c [new file with mode: 0644] blob
binaries/src/mafft/core/Falign_localhom.c [new file with mode: 0644] blob
binaries/src/mafft/core/Galign11.c [new file with mode: 0644] blob
binaries/src/mafft/core/Halignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/JTT.c [new file with mode: 0644] blob
binaries/src/mafft/core/Lalign11.c [new file with mode: 0644] blob
binaries/src/mafft/core/Lalign11.c.fast [new file with mode: 0644] blob
binaries/src/mafft/core/Lalign11.c_nostatic [new file with mode: 0644] blob
binaries/src/mafft/core/Lalignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/MSalign11.c [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.algAa [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.algLargeA [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.alga [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.algsmalla [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.back [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.bkbk [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.bug [new file with mode: 0644] blob
binaries/src/mafft/core/MSalignmm.c.work [new file with mode: 0644] blob
binaries/src/mafft/core/Makefile [new file with mode: 0644] blob
binaries/src/mafft/core/Qalignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/Ralignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/SAalignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/Salignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/addfunctions.c [new file with mode: 0644] blob
binaries/src/mafft/core/blosum.c [new file with mode: 0644] blob
binaries/src/mafft/core/blosum.h [new file with mode: 0644] blob
binaries/src/mafft/core/constants.c [new file with mode: 0644] blob
binaries/src/mafft/core/contrafoldwrap.c [new file with mode: 0644] blob
binaries/src/mafft/core/countlen.c [new file with mode: 0644] blob
binaries/src/mafft/core/defs.c [new file with mode: 0644] blob
binaries/src/mafft/core/disttbfast.c [new file with mode: 0644] blob
binaries/src/mafft/core/dndblast.c [new file with mode: 0644] blob
binaries/src/mafft/core/dndfast4.c [new file with mode: 0644] blob
binaries/src/mafft/core/dndfast7.c [new file with mode: 0644] blob
binaries/src/mafft/core/dndpre.c [new file with mode: 0644] blob
binaries/src/mafft/core/dndpre2.c [new file with mode: 0644] blob
binaries/src/mafft/core/dndpre_score.c [new file with mode: 0644] blob
binaries/src/mafft/core/dp.h [new file with mode: 0644] blob
binaries/src/mafft/core/dvtditr.c [new file with mode: 0644] blob
binaries/src/mafft/core/f2cl.c [new file with mode: 0644] blob
binaries/src/mafft/core/fft.c [new file with mode: 0644] blob
binaries/src/mafft/core/fft.h [new file with mode: 0644] blob
binaries/src/mafft/core/fftFunctions.c [new file with mode: 0644] blob
binaries/src/mafft/core/functions.h [new file with mode: 0644] blob
binaries/src/mafft/core/genGalign11.c [new file with mode: 0644] blob
binaries/src/mafft/core/genalign11.c [new file with mode: 0644] blob
binaries/src/mafft/core/getlag.c [new file with mode: 0644] blob
binaries/src/mafft/core/io.c [new file with mode: 0644] blob
binaries/src/mafft/core/iteration.c [new file with mode: 0644] blob
binaries/src/mafft/core/mafft-distance.c [new file with mode: 0644] blob
binaries/src/mafft/core/mafft-homologs.1 [new file with mode: 0644] blob
binaries/src/mafft/core/mafft-homologs.tmpl [new file with mode: 0644] blob
binaries/src/mafft/core/mafft-profile.c [new file with mode: 0644] blob
binaries/src/mafft/core/mafft.1 [new file with mode: 0644] blob
binaries/src/mafft/core/mafft.bat [new file with mode: 0644] blob
binaries/src/mafft/core/mafft.tmpl [new file with mode: 0644] blob
binaries/src/mafft/core/mafft.tmpl.subopt [new file with mode: 0644] blob
binaries/src/mafft/core/mccaskillwrap.c [new file with mode: 0644] blob
binaries/src/mafft/core/mingw64mingw32 [new file with mode: 0644] blob
binaries/src/mafft/core/miyata.h [new file with mode: 0644] blob
binaries/src/mafft/core/miyata5.h [new file with mode: 0644] blob
binaries/src/mafft/core/mltaln.h [new file with mode: 0644] blob
binaries/src/mafft/core/mltaln9.c [new file with mode: 0644] blob
binaries/src/mafft/core/mtxutl.c [new file with mode: 0644] blob
binaries/src/mafft/core/mtxutl.h [new file with mode: 0644] blob
binaries/src/mafft/core/multi2hat3s.c [new file with mode: 0644] blob
binaries/src/mafft/core/newick2mafft.rb [new file with mode: 0644] blob
binaries/src/mafft/core/nj.c [new file with mode: 0644] blob
binaries/src/mafft/core/pair2hat3s.c [new file with mode: 0644] blob
binaries/src/mafft/core/pairash.c [new file with mode: 0644] blob
binaries/src/mafft/core/pairlara.c [new file with mode: 0644] blob
binaries/src/mafft/core/pairlocalalign.c [new file with mode: 0644] blob
binaries/src/mafft/core/partQalignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/partSalignmm.c [new file with mode: 0644] blob
binaries/src/mafft/core/regtable2seq.c [new file with mode: 0644] blob
binaries/src/mafft/core/replaceu.c [new file with mode: 0644] blob
binaries/src/mafft/core/restoreu.c [new file with mode: 0644] blob
binaries/src/mafft/core/rna.c [new file with mode: 0644] blob
binaries/src/mafft/core/rnatest.c [new file with mode: 0644] blob
binaries/src/mafft/core/score.c [new file with mode: 0644] blob
binaries/src/mafft/core/seq2regtable.c [new file with mode: 0644] blob
binaries/src/mafft/core/setcore.c [new file with mode: 0644] blob
binaries/src/mafft/core/sextet5.c [new file with mode: 0644] blob
binaries/src/mafft/core/share.h [new file with mode: 0644] blob
binaries/src/mafft/core/splittbfast.c [new file with mode: 0644] blob
binaries/src/mafft/core/suboptalign11.c [new file with mode: 0644] blob
binaries/src/mafft/core/tbfast.c [new file with mode: 0644] blob
binaries/src/mafft/core/tddis.c [new file with mode: 0644] blob
binaries/src/mafft/core/tditeration.c [new file with mode: 0644] blob
binaries/src/mafft/core/test.c [new file with mode: 0644] blob
binaries/src/mafft/core/treeOperation.c [new file with mode: 0644] blob
binaries/src/mafft/core/univscript.tmpl [new file with mode: 0644] blob
binaries/src/mafft/extensions/Makefile [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/AlifoldMEA.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/BPPMatrix.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/Beta.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/GlobalParameters.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/Globaldp.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/Globaldp.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/Main.cc [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/Makefile [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/McCaskill.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/McCaskill.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/README [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/ScoreType.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/StemCandidate.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/Util.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/config.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/nrutil.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/params-weird [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/postProcessings.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/CompareToRef.cc [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Defaults.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Defaults.h_backup [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/EMtrainingALL.txt [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/EvolutionaryTree.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FileBuffer.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FixRef.cc [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Main.cc [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/MakeGnuPlot.cc [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Makefile [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/MultiSequence.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/ProbabilisticModel.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/ProjectPairwise.cc [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/README [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/SafeVector.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/ScoreType.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Sequence.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/SparseMatrix.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/mlparams0 [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/probconsRNA/train-script [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/scarna.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/seq2scs.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/vienna/COPYING [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_const.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_par.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.cpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/vienna/energy_param.hpp [new file with mode: 0644] blob
binaries/src/mafft/extensions/mxscarna_src/vienna/params.h [new file with mode: 0644] blob
binaries/src/mafft/extensions/univscript.tmpl [new file with mode: 0644] blob
binaries/src/mafft/license [new file with mode: 0644] blob
binaries/src/mafft/license.extensions [new file with mode: 0644] blob
binaries/src/mafft/readme [new file with mode: 0644] blob
binaries/src/mafft/test/sample [new file with mode: 0644] blob
binaries/src/mafft/test/sample.dpparttree [new file with mode: 0644] blob
binaries/src/mafft/test/sample.fftns2 [new file with mode: 0644] blob
binaries/src/mafft/test/sample.fftnsi [new file with mode: 0644] blob
binaries/src/mafft/test/sample.gins1 [new file with mode: 0644] blob
binaries/src/mafft/test/sample.ginsi [new file with mode: 0644] blob
binaries/src/mafft/test/sample.lins1 [new file with mode: 0644] blob
binaries/src/mafft/test/sample.linsi [new file with mode: 0644] blob
binaries/src/mafft/test/sample.parttree [new file with mode: 0644] blob
binaries/src/mafft/test/samplerna [new file with mode: 0644] blob
binaries/src/mafft/test/samplerna.qinsi [new file with mode: 0644] blob
binaries/src/mafft/test/samplerna.xinsi [new file with mode: 0644] blob