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JWS-112 Uploaded a new aacon jar, following a minor update made to AAcon's output format.

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    ./windows/compbio-conservation-1.1.jar
JWS-112 Hotfix the last t-coffee version 11. The -mode quickaln preset breaks if ’t_coffee’ is not found in $PATH. By calling t_coffee.sh instead, the problem is fixed by updating the $PATH on the flight and passing the original arguments to t_coffee.

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    ./src/tcoffee/t_coffee_source/t_coffee.sh
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JWS-112 Updated AACon to version 1.1.

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    ./windows/compbio-conservation-1.1.jar
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JWS-117 Compiled all tools with ./compilebin.sh and some were missing related files.

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    ./src/GLProbs-1.0/MSA.o
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    ./src/GLProbs-1.0/MSAClusterTree.o
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    ./src/GLProbs-1.0/MSAGuideTree.o
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    ./src/GLProbs-1.0/MSAPartProbs.o
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    ./src/GLProbs-1.0/MSAReadMatrix.o
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    ./src/GLProbs-1.0/main.o
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    ./src/MSAProbs-0.9.7/MSAProbs/MSA.o
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    ./src/MSAProbs-0.9.7/MSAProbs/MSAClusterTree.o
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    ./src/MSAProbs-0.9.7/MSAProbs/MSAGuideTree.o
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    ./src/MSAProbs-0.9.7/MSAProbs/MSAPartProbs.o
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    ./src/MSAProbs-0.9.7/MSAProbs/MSAReadMatrix.o
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    ./src/MSAProbs-0.9.7/MSAProbs/main.o
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    ./src/MSAProbs-0.9.7/MSAProbs/msaprobs
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    ./src/ViennaRNA/H/Makefile
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JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

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    ./src/tcoffee/bin/binaries/linux/t_coffee
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    ./src/tcoffee/example/1D4V-1.pdb
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    ./src/tcoffee/example/1D4V-2.pdb
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    ./src/tcoffee/example/1D4V-3.pdb
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    ./src/tcoffee/example/1EXT-1.pdb
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    ./src/tcoffee/example/1EXT-2.pdb
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    ./src/tcoffee/example/1EXT-3.pdb
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    ./src/tcoffee/example/1EXT-4.pdb
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    ./src/tcoffee/example/1JMA-1.pdb
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    ./src/tcoffee/example/1JMA-2.pdb
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    ./src/tcoffee/example/1OQE-1.pdb
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    ./src/tcoffee/example/1SG1-1.pdb
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    ./src/tcoffee/example/1SG1-2.pdb
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    ./src/tcoffee/example/1SG1-3.pdb
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JWS-112 Bumping version of Mafft to version 7.310.

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    ./src/mafft/binaries/contrafoldwrap
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    ./src/mafft/binaries/mafft-distance
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    ./src/mafft/binaries/mafftash_premafft.pl
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    ./src/mafft/binaries/makedirectionlist
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JWS-112 Bumping version of ClustalW (src, binaries and windows) to version 2.1.

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    ./src/clustalw/config.log
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    ./src/clustalw/config.status
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    ./src/clustalw/configure
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JWS-112 Bumping version of ClustalO (src, binaries and windows) to version 1.2.4.

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    ./src/clustalo/Makefile
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    ./src/clustalo/_configs.sed
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    ./src/clustalo/clustalo.pc
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    ./src/clustalo/config.log
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    ./src/clustalo/config.status
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    ./src/clustalo/libtool
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JWS-113 Commented Jpred entries in various configuration files.

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Add an old jpred.pl script

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    ./src/jpred/jpred_old.pl
Re-design jpred.pl input options: no -seq for a file with 1 FASTA record only.

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Remove difinition of UNIREF for JABAWS from jpred.pl

Fix bug with DB checking in jpred.pl

Fix problem with old Probcons code: couldn't be complied with modern gcc since string.h is needed

Replace binaries with one compatible with the dundee cluster

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    ./src/MSAProbs-0.9.7/MSAProbs/msaprobs
Add GLprobs and MSAprobs to binaries

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    ./src/GLProbs-1.0/Defaults.h
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    ./src/GLProbs-1.0/FileBuffer.h
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    ./src/GLProbs-1.0/MSA.cpp
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    ./src/GLProbs-1.0/MSA.h
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    ./src/GLProbs-1.0/MSA2.cpp
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    ./src/GLProbs-1.0/MSAClusterTree.cpp
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    ./src/GLProbs-1.0/MSAClusterTree.h
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    ./src/GLProbs-1.0/MSADef.h
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    ./src/GLProbs-1.0/MSAGuideTree.cpp
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    ./src/GLProbs-1.0/MSAGuideTree.h
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    ./src/GLProbs-1.0/MSAPartProbs.cpp
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    ./src/GLProbs-1.0/MSAProbs.vcproj
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    ./src/GLProbs-1.0/MSAProbs.vcproj.STUDENT.LIUY0039.user
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    ./src/GLProbs-1.0/MSAReadMatrix.cpp
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    ./src/GLProbs-1.0/MSAReadMatrix.h
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New Linux binaries for ViennaRNA

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Set right path to UNIREF at ningal

Set right permissions for Jpred binaries

Made the binary executable at ningal

Add SS prediction for multiple aligment into jpred.pl. Before this was a part of another script

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    ./src/jpred/tests/alignment.clustal
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    ./src/jpred/tests/alignment.fasta
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    ./src/jpred/tests/alignment.msf
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    ./src/jpred/tests/d1b3aa_.fas
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    ./src/jpred/tests/res_d16vpa_.align
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    ./src/jpred/tests/res_d16vpa_.concise
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    ./src/jpred/tests/res_d16vpa_.hmm
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    ./src/jpred/tests/res_d16vpa_.profile
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    ./src/jpred/tests/res_d16vpa_.pssm
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    ./src/jpred/tests/res_d16vpa_.res
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    ./src/jpred/tests/res_d16vpa_.res.fasta
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    ./src/jpred/x86_64/alscript
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    ./src/jpred/x86_64/readseq
Fix problem with path to the UNIREF database

Add missing binaty and statis library

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    ./src/ViennaRNA/Kinfold/Kinfold
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    ./src/ViennaRNA/lib/libRNA.a
Add missing doc files

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    ./src/ViennaRNA/doc/doxygen.conf
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    ./src/ViennaRNA/doc/html/sync_off.png
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    ./src/ViennaRNA/doc/html/sync_on.png
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    ./src/ViennaRNA/doc/latex/1_88_84__epars_8h.tex
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    ./src/ViennaRNA/doc/latex/1_88_84__epars_8h_source.tex
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    ./src/ViennaRNA/doc/latex/1_88_84__intloops_8h.tex
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    ./src/ViennaRNA/doc/latex/1_88_84__intloops_8h_source.tex
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    ./src/ViennaRNA/doc/latex/2Dfold_8h.tex
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    ./src/ViennaRNA/doc/latex/2Dfold_8h__incl.md5
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    ./src/ViennaRNA/doc/latex/2Dfold_8h__incl.pdf
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    ./src/ViennaRNA/doc/latex/2Dfold_8h_source.tex
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    ./src/ViennaRNA/doc/latex/2Dpfold_8h.tex
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    ./src/ViennaRNA/doc/latex/2Dpfold_8h__incl.md5
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    ./src/ViennaRNA/doc/latex/2Dpfold_8h__incl.pdf
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    ./src/ViennaRNA/doc/latex/2Dpfold_8h_source.tex
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Replace Progs/RNAalifold with x64 binary and add all other programs

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    ./src/ViennaRNA/Progs/RNA2Dfold
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    ./src/ViennaRNA/Progs/RNALalifold
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    ./src/ViennaRNA/Progs/RNALfold
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    ./src/ViennaRNA/Progs/RNAPKplex
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    ./src/ViennaRNA/Progs/RNAaliduplex
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    ./src/ViennaRNA/Progs/RNAcofold
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    ./src/ViennaRNA/Progs/RNAdistance
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    ./src/ViennaRNA/Progs/RNAduplex
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    ./src/ViennaRNA/Progs/RNAeval
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    ./src/ViennaRNA/Progs/RNAfold
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    ./src/ViennaRNA/Progs/RNAheat
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    ./src/ViennaRNA/Progs/RNAinverse
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    ./src/ViennaRNA/Progs/RNApaln
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    ./src/ViennaRNA/Progs/RNAparconv
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JWS-69 RNAalifold Linux Binary

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    ./src/ViennaRNA/Progs/RNAalifold
conf/Executable.properties and compilebin.sh updated for linux.

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WSTester updated to work plus hopefully all the other changes that need to go into the remote.

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    ./src/ViennaRNA/AUTHORS
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    ./src/ViennaRNA/COPYING
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    ./src/ViennaRNA/ChangeLog
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    ./src/ViennaRNA/Cluster/AD_main.c
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    ./src/ViennaRNA/Cluster/AS_main.c
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    ./src/ViennaRNA/Cluster/AnalyseDists.1
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    ./src/ViennaRNA/Cluster/AnalyseSeqs.1
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    ./src/ViennaRNA/Cluster/Makefile.am
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    ./src/ViennaRNA/Cluster/Makefile.in
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    ./src/ViennaRNA/Cluster/PS3D.c
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    ./src/ViennaRNA/Cluster/PS3D.h
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    ./src/ViennaRNA/Cluster/StrEdit_CostMatrix.h
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    ./src/ViennaRNA/Cluster/cluster.c
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    ./src/ViennaRNA/Cluster/cluster.h
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    ./src/ViennaRNA/Cluster/distance_matrix.c
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Add results of tests of Jpred

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    ./src/jpred/tests/res_d16vpa_.res.fasta
Modify Jpred for JABAWS