├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── changelog.md ├── clustal-omega-1.2.0 └── clustalO-64bit ├── examples ├── MUSI │ └── musi.fa └── antibodies │ └── antibodies.fa ├── galaxy ├── Hammock │ └── settings │ │ ├── misc │ │ └── blosum62.freq_rownorm │ │ └── settings.prop ├── external_tools │ ├── darwin │ │ ├── clustal-omega-1.2.0-macosx │ │ ├── hhmake │ │ ├── hhsearch │ │ ├── hmmbuild │ │ ├── hmmsearch │ │ └── lib │ │ │ ├── ._hh │ │ │ ├── ._libffindex.so.0.1 │ │ │ ├── hh │ │ │ ├── ._bin │ │ │ ├── ._data │ │ │ ├── ._scripts │ │ │ ├── bin │ │ │ │ ├── ._cstranslate │ │ │ │ └── cstranslate │ │ │ └── data │ │ │ │ ├── ._context_data.lib │ │ │ │ ├── ._cs219.lib │ │ │ │ ├── ._do_not_delete │ │ │ │ ├── ._do_not_delete.phr │ │ │ │ ├── ._do_not_delete.pin │ │ │ │ ├── ._do_not_delete.psq │ │ │ │ ├── context_data.lib │ │ │ │ ├── cs219.lib │ │ │ │ ├── do_not_delete │ │ │ │ ├── do_not_delete.phr │ │ │ │ ├── do_not_delete.pin │ │ │ │ └── do_not_delete.psq │ │ │ └── libffindex.so.0.1 │ └── linux │ │ ├── clustalo-1.2.0-Ubuntu-x86_64 │ │ ├── hhmake │ │ ├── hhsearch │ │ ├── hmmbuild │ │ ├── hmmsearch │ │ └── lib │ │ └── hh │ │ ├── bin │ │ └── cstranslate │ │ └── data │ │ ├── context_data.lib │ │ ├── cs219.lib │ │ ├── do_not_delete │ │ ├── do_not_delete.phr │ │ ├── do_not_delete.pin │ │ └── do_not_delete.psq ├── hammock.xml ├── tool_dependencies.xml └── wrapper.sh ├── hhsuite-2.0.16 ├── CHANGES ├── LICENSE ├── README ├── bin │ ├── hhmake │ └── hhsearch ├── data │ ├── context_data.lib │ ├── cs219.lib │ ├── do_not_delete │ ├── do_not_delete.phr │ ├── do_not_delete.pin │ ├── do_not_delete.psq │ ├── query.a3m │ ├── query.hhm │ ├── query.hhr │ └── query.seq ├── hhsuite-userguide.pdf ├── include │ ├── ffindex.h │ └── ffutil.h ├── lib │ └── hh │ │ ├── bin │ │ └── cstranslate │ │ └── data │ │ ├── context_data.lib │ │ ├── cs219.lib │ │ ├── do_not_delete │ │ ├── do_not_delete.phr │ │ ├── do_not_delete.pin │ │ └── do_not_delete.psq ├── lib64 │ ├── libffindex.a │ ├── libffindex.so │ └── libffindex.so.0.1 └── scripts │ ├── Align.pm │ ├── HHPaths.pm │ ├── addss.pl │ ├── create_profile_from_hhm.pl │ ├── create_profile_from_hmmer.pl │ ├── hhblitsdb.pl │ ├── hhmakemodel.pl │ ├── multithread.pl │ ├── pdb2fasta.pl │ ├── pdbfilter.pl │ ├── reformat.pl │ ├── renumberpdb.pl │ └── splitfasta.pl ├── hmmer-3.1b1 └── src │ ├── hmmbuild │ └── hmmsearch ├── manifest.mf ├── manual.pdf ├── manual ├── biblio.bib └── manual.tex ├── matrices ├── blosum100.txt ├── blosum30.txt ├── blosum35.txt ├── blosum40.txt ├── blosum45.txt ├── blosum50.txt ├── blosum55.txt ├── blosum60.txt ├── blosum62.txt ├── blosum62.txt~ ├── blosum65.txt ├── blosum70.txt ├── blosum75.txt ├── blosum80.txt ├── blosum85.txt ├── blosum90.txt ├── gonnet250.txt ├── mcla71.txt └── pam250.txt ├── nbproject ├── build-impl.xml ├── genfiles.properties ├── project.properties └── project.xml ├── settings ├── misc │ ├── blosum62.freq_rownorm │ ├── empirical_probabs_Ph.D.-12.tsv │ ├── 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