Wrapper for Clustal Omega.
authorpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Wed, 3 Aug 2011 17:06:32 +0000 (17:06 +0000)
committerpvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Wed, 3 Aug 2011 17:06:32 +0000 (17:06 +0000)
commit35947b9e0b6ae1be74f17d15cd6a65ceadc6d310
treedc9f46d534d7e1201707652a91a09048837626b8
parente7bf02d1c203bc8d88b9095e89d5ca6cce21a882
Wrapper for Clustal Omega.

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4458 e3abac25-378b-4346-85de-24260fe3988d
183 files changed:
ExecutionStatistic/log/log.ctrl
ExecutionStatistic/log/log10.dat
ExecutionStatistic/log/logmirror.ctrl
ExecutionStatistic/seg0/c470.dat
ExecutionStatistic/seg0/c481.dat
ExecutionStatistic/seg0/c90.dat
binaries/src/clustalo/AUTHORS [new file with mode: 0644]
binaries/src/clustalo/COPYING [new file with mode: 0644]
binaries/src/clustalo/ChangeLog [new file with mode: 0644]
binaries/src/clustalo/Doxyfile [new file with mode: 0644]
binaries/src/clustalo/Doxyfile.in [new file with mode: 0644]
binaries/src/clustalo/INSTALL [new file with mode: 0644]
binaries/src/clustalo/Makefile.am [new file with mode: 0644]
binaries/src/clustalo/Makefile.in [new file with mode: 0644]
binaries/src/clustalo/NEWS [new file with mode: 0644]
binaries/src/clustalo/README [new file with mode: 0644]
binaries/src/clustalo/TODO [new file with mode: 0644]
binaries/src/clustalo/aclocal.m4 [new file with mode: 0644]
binaries/src/clustalo/clustalo.pc.in [new file with mode: 0644]
binaries/src/clustalo/config.guess [new file with mode: 0644]
binaries/src/clustalo/config.sub [new file with mode: 0644]
binaries/src/clustalo/configure [new file with mode: 0644]
binaries/src/clustalo/configure.ac [new file with mode: 0644]
binaries/src/clustalo/depcomp [new file with mode: 0644]
binaries/src/clustalo/install-sh [new file with mode: 0644]
binaries/src/clustalo/ltmain.sh [new file with mode: 0644]
binaries/src/clustalo/m4/ax_openmp.m4 [new file with mode: 0644]
binaries/src/clustalo/m4/ax_prefix_config_h.m4 [new file with mode: 0644]
binaries/src/clustalo/m4/libtool.m4 [new file with mode: 0644]
binaries/src/clustalo/m4/ltoptions.m4 [new file with mode: 0644]
binaries/src/clustalo/m4/ltsugar.m4 [new file with mode: 0644]
binaries/src/clustalo/m4/ltversion.m4 [new file with mode: 0644]
binaries/src/clustalo/m4/lt~obsolete.m4 [new file with mode: 0644]
binaries/src/clustalo/missing [new file with mode: 0644]
binaries/src/clustalo/src/Makefile.am [new file with mode: 0644]
binaries/src/clustalo/src/Makefile.in [new file with mode: 0644]
binaries/src/clustalo/src/clustal-omega-config.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal-omega.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal-omega.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/Makefile.am [new file with mode: 0644]
binaries/src/clustalo/src/clustal/Makefile.in [new file with mode: 0644]
binaries/src/clustalo/src/clustal/hhalign_wrapper.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/hhalign_wrapper.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/ktuple_pair.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/ktuple_pair.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/list.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/list.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/log.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/log.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/mbed.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/mbed.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/muscle_tree.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/muscle_tree.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/muscle_upgma.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/muscle_upgma.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/pair_dist.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/pair_dist.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/progress.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/progress.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/queue.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/seq.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/seq.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/symmatrix.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/symmatrix.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/tree.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/tree.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/util.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/util.h [new file with mode: 0644]
binaries/src/clustalo/src/clustal/weights.c [new file with mode: 0644]
binaries/src/clustalo/src/clustal/weights.h [new file with mode: 0644]
binaries/src/clustalo/src/clustalo-api-test.c [new file with mode: 0644]
binaries/src/clustalo/src/config.h.in [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/Makefile.am [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/Makefile.in [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/general.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hash-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hash.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhalign.cpp [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhalign.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhalignment-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhalignment.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhdecl-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhfullalignment-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhfullalignment.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhfunc-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhfunc.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhalfalignment-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhalfalignment.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhit-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhit.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhitlist-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhitlist.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhmm-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhhmm.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhmatrices-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/hhutil-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/list-C.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/list.h [new file with mode: 0644]
binaries/src/clustalo/src/hhalign/util-C.h [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/KMeans.cpp [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/KMeans.h [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/KmTree.cpp [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/KmTree.h [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/KmUtils.cpp [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/KmUtils.h [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/Makefile.am [new file with mode: 0644]
binaries/src/clustalo/src/kmpp/Makefile.in [new file with mode: 0644]
binaries/src/clustalo/src/main.cpp [new file with mode: 0644]
binaries/src/clustalo/src/mymain.c [new file with mode: 0644]
binaries/src/clustalo/src/mymain.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/00README [new file with mode: 0644]
binaries/src/clustalo/src/squid/COPYRIGHT [new file with mode: 0644]
binaries/src/clustalo/src/squid/LICENSE [new file with mode: 0644]
binaries/src/clustalo/src/squid/Makefile.am [new file with mode: 0644]
binaries/src/clustalo/src/squid/Makefile.in [new file with mode: 0644]
binaries/src/clustalo/src/squid/a2m.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/aligneval.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/alignio.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/clustal.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/clustalo.README [new file with mode: 0644]
binaries/src/clustalo/src/squid/cluster.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/dayhoff.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/eps.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/file.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/getopt.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/gki.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/gki.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/gsi.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/gsi.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/gsi64.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/gsi64.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/hsregex.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/iupac.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/msa.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/msa.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/msf.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/phylip.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/revcomp.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/rk.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/rk.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/selex.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/seqencode.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/shuffle.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/sqerror.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/sqfuncs.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/sqio.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/squid-1.9g.tar.gz [new file with mode: 0644]
binaries/src/clustalo/src/squid/squid.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/squidcore.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/sre_ctype.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/sre_math.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/sre_random.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/sre_random.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/sre_string.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/ssi.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/ssi.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/stack.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/stockholm.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/stockholm.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/stopwatch.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/stopwatch.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/translate.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/types.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/vectorops.c [new file with mode: 0644]
binaries/src/clustalo/src/squid/vectorops.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/version.h [new file with mode: 0644]
binaries/src/clustalo/src/squid/weight.c [new file with mode: 0644]
binaries/windows/clustalo/AUTHORS.txt [new file with mode: 0644]
binaries/windows/clustalo/COPYING.txt [new file with mode: 0644]
binaries/windows/clustalo/ChangeLog.txt [new file with mode: 0644]
binaries/windows/clustalo/INSTALL.txt [new file with mode: 0644]
binaries/windows/clustalo/README.txt [new file with mode: 0644]
binaries/windows/clustalo/clustalo.exe [new file with mode: 0644]
binaries/windows/clustalo/issues.txt [new file with mode: 0644]
binaries/windows/clustalo/libgomp-1.dll [new file with mode: 0644]
binaries/windows/clustalo/mingwm10.dll [new file with mode: 0644]
binaries/windows/clustalo/pthreadGC2.dll [new file with mode: 0644]
conf/Executable.properties
conf/settings/ClustaloLimits.xml [new file with mode: 0644]
conf/settings/ClustaloParameters.xml [new file with mode: 0644]
conf/settings/ClustaloPresets.xml [new file with mode: 0644]
runner/compbio/runner/msa/ClustalO.java [new file with mode: 0644]
testsrc/compbio/runner/msa/ClustalOTester.java [new file with mode: 0644]