├── .github ├── .DS_Store └── workflows │ ├── release.yml │ └── update_release_table.py ├── .gitignore ├── .travis.yml ├── INSTALL ├── LICENSE ├── Makefile.in ├── README.md ├── autobuild ├── 00README ├── autobuild.pl ├── hmmer_autobuilds.pl ├── intel-linux-gcc ├── intel-linux-gcc-ubuntu32 ├── intel-linux-icc-ia32-mpi ├── intel-linux-icc-intel64-mpi ├── intel-macosx-gcc ├── intel-macosx-gcc-debug ├── ppc-aix-xlc └── ppc-macosx ├── config.guess ├── config.sub ├── configure.ac ├── contrib ├── p7_thermo.c └── p7_thermo.h ├── documentation ├── Makefile.in ├── man │ ├── Makefile.in │ ├── alimask.man.in │ ├── hmmalign.man.in │ ├── hmmbuild.man.in │ ├── hmmc2.man.in │ ├── hmmconvert.man.in │ ├── hmmemit.man.in │ ├── hmmer.man.in │ ├── hmmfetch.man.in │ ├── hmmlogo.man.in │ ├── hmmpgmd.man.in │ ├── hmmpgmd_shard.man.in │ ├── hmmpress.man.in │ ├── hmmscan.man.in │ ├── hmmscant.man.in │ ├── hmmsearch.man.in │ ├── hmmsearcht.man.in │ ├── hmmsim.man.in │ ├── hmmstat.man.in │ ├── jackhmmer.man.in │ ├── makehmmerdb.man.in │ ├── nhmmer.man.in │ ├── nhmmscan.man.in │ └── phmmer.man.in └── userguide │ ├── Makefile.in │ ├── ack.tex │ ├── copyright.tex.in │ ├── daemon.tex │ ├── distilled.bib │ ├── formats.tex │ ├── glossary.tex │ ├── hmmbuild.tex │ ├── hmmc.tex │ ├── inclusions │ ├── Makefile.in │ ├── alidisplay-serialize.ai │ ├── alidisplay-serialize.pdf │ ├── daemon-results.ai │ ├── daemon-results.pdf │ ├── daemon.ai │ ├── daemon.pdf │ ├── domain-serialize.ai │ ├── domain-serialize.pdf │ ├── gen-inclusions.py │ ├── globins4.sto │ ├── hit-serialize.ai │ ├── hit-serialize.pdf │ ├── hmmalign-globins.out │ ├── hmmalign-globins.out2 │ ├── hmmbuild-Pkinase.out │ ├── hmmbuild-globins.out │ ├── hmmbuild-globins.out2 │ ├── hmmbuild-made1.out │ ├── hmmbuild-noargs.out │ ├── hmmc2.out │ ├── hmmc2_2.out │ ├── hmmpgmd-search-stats-serialize.ai │ ├── hmmpgmd-search-stats-serialize.pdf │ ├── hmmpress-minifam.out │ ├── hmmscan-minifam-sevenless.out │ ├── hmmscan-minifam-sevenless.out2 │ ├── hmmscan-minifam-sevenless.out3 │ ├── hmmscan-noargs.out │ ├── hmmsearch-fn3-sevenless.out │ ├── hmmsearch-fn3-sevenless.out2 │ ├── hmmsearch-fn3-sevenless.out3 │ ├── hmmsearch-fn3-sevenless.out4 │ ├── hmmsearch-fn3-uniprot.out │ ├── hmmsearch-globins.out │ ├── hmmsearch-globins.out2 │ ├── hmmsearch-globins.out3 │ ├── hmmsearcht-pkinase.out │ ├── hmmsearcht-pkinase.out2 │ ├── hmmsearcht-pkinase.out3 │ ├── hmmsearcht-pkinase.out4 │ ├── hmmstat-minifam.out │ ├── inclusions.def │ ├── jackhmmer-hbb-uniprot.out │ ├── jackhmmer-hbb-uniprot.out2 │ ├── jackhmmer-hbb-uniprot.out3 │ ├── jackhmmer-hbb-uniprot.out4 │ ├── jackhmmer-hbb-uniprot.out5 │ ├── jackhmmer-hbb-uniprot.out6 │ ├── jackhmmer-hbb-uniprot.out7 │ ├── nhmmer-made1.out │ ├── nhmmer-made1.out2 │ ├── nhmmer-made1.out3 │ ├── nhmmer-made1.out4 │ ├── nhmmer-made1.out5 │ └── sevenless_domains.out │ ├── install.tex │ ├── installation.md │ ├── introduction.tex │ ├── macros.tex │ ├── main.tex │ ├── pipeline.tex │ ├── tabular.tex │ ├── titlepage.tex.in │ ├── titlepage_daemon.tex.in │ ├── tufte-book.cls │ ├── tufte-common-local.tex │ ├── tufte-common.def │ ├── tutorial.md │ ├── tutorial.tex │ └── unsrtnat-brief.bst ├── install-sh ├── libdivsufsort ├── AUTHORS ├── COPYING ├── Makefile.in ├── README ├── VERSION ├── divsufsort.c └── divsufsort.h.in ├── makeTAGS.sh ├── release-notes ├── 00CHECKLIST ├── ANNOUNCE-1.8 ├── ANNOUNCE-2.1 ├── HISTORY ├── LICENSE.sh ├── RELEASE-1.5 ├── RELEASE-1.6 ├── RELEASE-1.7 ├── RELEASE-1.8 ├── RELEASE-1.8.3 ├── RELEASE-1.8.4 ├── RELEASE-2.0 ├── RELEASE-2.1 ├── RELEASE-2.1.1 ├── RELEASE-2.1.2 ├── RELEASE-2.1.3 ├── RELEASE-2.2 ├── RELEASE-2.3 ├── RELEASE-2.3.1 ├── RELEASE-2.3.2 ├── RELEASE-2.3.3 ├── RELEASE-3.0 ├── RELEASE-3.0a2 ├── RELEASE-3.0b1 ├── RELEASE-3.0b2 ├── RELEASE-3.0b3 ├── RELEASE-3.0rc1 ├── RELEASE-3.0rc2 ├── RELEASE-3.1b1 ├── RELEASE-3.1b2 ├── RELEASE-3.1rc1 ├── RELEASE-3.2 ├── RELEASE-3.2.1 ├── RELEASE-3.3.1.md ├── RELEASE-3.3.2.md └── RELEASE-3.3.md ├── src ├── Makefile.in ├── bathbuild.c ├── bathconvert.c ├── bathfetch.c ├── bathsearch.c ├── bathstat.c ├── build.c ├── cachedb.c ├── cachedb.h ├── cachedb_shard.c ├── cachedb_shard.h ├── decoding_frameshift.c ├── emit.c ├── errors.c ├── evalues.c ├── eweight.c ├── fm_alphabet.c ├── fm_general.c ├── fm_sse.c ├── fm_ssv.c ├── fwdback_frameshift.c ├── generic_decoding.c ├── generic_fwdback.c ├── generic_fwdback_banded.c ├── generic_fwdback_chk.c ├── generic_fwdback_rescaled.c ├── generic_msv.c ├── generic_null2.c ├── generic_optacc.c ├── generic_stotrace.c ├── generic_viterbi.c ├── generic_vtrace.c ├── h2_io.c ├── heatmap.c ├── hmmc2.c ├── hmmd_search_status.c ├── hmmdmstr.c ├── hmmdmstr_shard.c ├── hmmdutils.c ├── hmmdwrkr.c ├── hmmdwrkr_shard.c ├── hmmemit.c ├── hmmer.c ├── hmmer.h ├── hmmerfm-exactmatch.c ├── hmmpgmd.c ├── hmmpgmd.h ├── hmmpgmd2msa.c ├── hmmpgmd_client_example.pl ├── hmmpgmd_shard.c ├── hmmpgmd_shard.h ├── hmmpress.itest.pl ├── impl_neon │ ├── 00MANIFEST │ ├── Makefile.in │ ├── decoding.c │ ├── fwdback.c │ ├── impl_neon.h │ ├── io.c │ ├── mpi.c │ ├── msvfilter.c │ ├── null2.c │ ├── optacc.c │ ├── p7_omx.c │ ├── p7_oprofile.c │ ├── ssvfilter.c │ ├── stotrace.c │ ├── vitfilter.c │ └── vitscore.c ├── impl_sse │ ├── 00MANIFEST │ ├── Makefile.in │ ├── decoding.c │ ├── fbparsers.tex │ ├── fwdback.c │ ├── impl_sse.h │ ├── io.c │ ├── mpi.c │ ├── msvfilter.c │ ├── null2.c │ ├── optacc.c │ ├── p7_omx.ai │ ├── p7_omx.c │ ├── p7_oprofile.c │ ├── ssvfilter.c │ ├── stotrace.c │ ├── vitfilter.c │ └── vitscore.c ├── impl_vmx │ ├── 00MANIFEST │ ├── Makefile.in │ ├── decoding.c │ ├── fwdback.c │ ├── impl_vmx.h │ ├── io.c │ ├── mpi.c │ ├── msvfilter.c │ ├── null2.c │ ├── optacc.c │ ├── p7_omx.c │ ├── p7_oprofile.c │ ├── stotrace.c │ ├── vitfilter.c │ └── vitscore.c ├── itest_brute.c ├── logsum.c ├── modelconfig.c ├── modelstats.c ├── mpisupport.c ├── null2_frameshift.c ├── optacc_frameshift.c ├── p7_alidisplay.c ├── p7_bg.c ├── p7_builder.c ├── p7_config.h.in ├── p7_domain.c ├── p7_domaindef.c ├── p7_gbands.c ├── p7_gbands.h ├── p7_gmx.c ├── p7_gmx_fs.c ├── p7_gmxb.c ├── p7_gmxb.h ├── p7_gmxchk.c ├── p7_gmxchk.h ├── p7_hit.c ├── p7_hmm.c ├── p7_hmmcache.c ├── p7_hmmcache.h ├── p7_hmmd_search_stats.c ├── p7_hmmfile.c ├── p7_hmmwindow.c ├── p7_null3.c ├── p7_pipeline.c ├── p7_prior.c ├── p7_profile.c ├── p7_scoredata.c ├── p7_search_builder.c ├── p7_spensemble.c ├── p7_tophits.c ├── p7_trace.c ├── phmmert.dSYM │ └── Contents │ │ ├── Info.plist │ │ └── Resources │ │ └── DWARF │ │ └── phmmert ├── seqmodel.c ├── stotrace_frameshift.c └── tracealign.c ├── testsuite ├── 20aa-alitest.afa ├── 20aa-alitest.fa ├── 20aa-alitest.phr ├── 20aa-alitest.pin ├── 20aa-alitest.pog ├── 20aa-alitest.psd ├── 20aa-alitest.psi ├── 20aa-alitest.psq ├── 20aa-alitest.sto ├── 20aa.bhmm ├── 20aa.hmm ├── 20aa.sto ├── 2OG-FeII_Oxy_3-nt.fa ├── 2OG-FeII_Oxy_3-nt.hmm ├── 2OG-FeII_Oxy_3.bhmm ├── 2OG-FeII_Oxy_3.fa ├── 2OG-FeII_Oxy_3.hmm ├── 2OG-FeII_Oxy_3.sto ├── 3box-alitest.fa ├── 3box-alitest.nhr ├── 3box-alitest.nin ├── 3box-alitest.nog ├── 3box-alitest.nsd ├── 3box-alitest.nsi ├── 3box-alitest.nsq ├── 3box.hmm ├── 3box.sto ├── Caudal_act-10.fa ├── Caudal_act-nt.fa ├── Caudal_act.bhmm ├── Caudal_act.hmm ├── Caudal_act.sto ├── LuxC.hmm ├── LuxC.sto ├── M1.hmm ├── M1.sto ├── MYG_ESCGI_dna_hmmscant.txt ├── Makefile.in ├── PAX8_HUMAN ├── PSE.hmm ├── PSE.sto ├── Patched.hmm ├── Patched.sto ├── RRM_1-10.fa ├── RRM_1.bhmm ├── RRM_1.hmm ├── RRM_1.sto ├── SMC_N.hmm ├── SMC_N.sto ├── XYPPX.hmm ├── XYPPX.sto ├── ecori.fa ├── ecori.hmm ├── ecori.sto ├── globins4.sto ├── globins45-nt.fa ├── h3.pm ├── i1-build-variation.sh ├── i10-duplicate-names.pl ├── i11-hmmalign-mapali.pl ├── i12-delete-corruption.pl ├── i13-msa-integrity.pl ├── i14-hmmemit-consensus.pl ├── i15-hmmconvert.pl ├── i16-build-allins.pl ├── i17-stdin.pl ├── i18-nhmmer-generic.pl ├── i19-hmmpgmd-ga.pl ├── i2-search-variation.sh ├── i20-fmindex-core.pl ├── i21-rewind.pl ├── i22-hmmpgmd-shard-ga.pl ├── 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