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Changes
ignore.txt
lib/Bio/HMM/Logo.c
lib/Bio/HMM/Logo.pm
lib/Bio/HMM/Logo.typemap
lib/Bio/HMM/Logo/Fonts/LICENSE.txt
lib/Bio/HMM/Logo/Fonts/SourceCodePro-Bold.ttf
lib/Bio/HMM/Logo/Fonts/SourceCodePro-Semibold.ttf
Makefile.PL
MANIFEST This list of files
README
README.md
scripts/test_logo_gen
src/aclocal.m4
src/autobuild/00README
src/autobuild/autobuild.pl
src/autobuild/hmmer_autobuilds.pl
src/autobuild/intel-linux-gcc
src/autobuild/intel-linux-gcc-ubuntu32
src/autobuild/intel-linux-icc-ia32-mpi
src/autobuild/intel-linux-icc-intel64-mpi
src/autobuild/intel-macosx-gcc
src/autobuild/intel-macosx-gcc-debug
src/autobuild/intel-macosx-gcc-dummy
src/autobuild/ppc-aix-xlc
src/autobuild/ppc-macosx
src/bugs/BUGTRAX
src/config.guess
src/config.sub
src/configure
src/configure.ac
src/contrib/p7_thermo.c
src/contrib/p7_thermo.h
src/COPYRIGHT
src/documentation/Makefile.in
src/documentation/man/alimask.man
src/documentation/man/boilerplate-tail
src/documentation/man/hmmalign.man
src/documentation/man/hmmbuild.man
src/documentation/man/hmmconvert.man
src/documentation/man/hmmemit.man
src/documentation/man/hmmer.man
src/documentation/man/hmmfetch.man
src/documentation/man/hmmpgmd.man
src/documentation/man/hmmpress.man
src/documentation/man/hmmscan.man
src/documentation/man/hmmsearch.man
src/documentation/man/hmmsim.man
src/documentation/man/hmmstat.man
src/documentation/man/jackhmmer.man
src/documentation/man/Makefile.in
src/documentation/man/nhmmer.man
src/documentation/man/nhmmscan.man
src/documentation/man/phmmer.man
src/documentation/userguide/ack.tex
src/documentation/userguide/copyright.tex.in
src/documentation/userguide/formats.tex
src/documentation/userguide/glossary.tex
src/documentation/userguide/hmmbuild.tex
src/documentation/userguide/install.tex
src/documentation/userguide/introduction.tex
src/documentation/userguide/macros.tex
src/documentation/userguide/main.tex
src/documentation/userguide/Makefile.in
src/documentation/userguide/more.tex
src/documentation/userguide/pipeline.tex
src/documentation/userguide/tabular.tex
src/documentation/userguide/titlepage.tex.in
src/documentation/userguide/tutorial.tex
src/easel/00CHECKLIST
src/easel/00README
src/easel/aclocal.m4
src/easel/BUGTRAX
src/easel/config.guess
src/easel/config.sub
src/easel/configure.ac
src/easel/COPYRIGHT
src/easel/demotic/00README
src/easel/demotic/blast2profmark
src/easel/demotic/blast2tbl
src/easel/demotic/demotic_blast.pm
src/easel/demotic/demotic_fasta.pm
src/easel/demotic/demotic_h2.pm
src/easel/demotic/demotic_hmmer.pm
src/easel/demotic/demotic_infernal_tab.pm
src/easel/demotic/examples/example-single-psiquery.fa
src/easel/demotic/examples/example-single.asnt
src/easel/demotic/examples/example-single.fa
src/easel/demotic/examples/example-single.fa.phr
src/easel/demotic/examples/example-single.fa.pin
src/easel/demotic/examples/example-single.fa.psq
src/easel/demotic/examples/example-single.pbl
src/easel/demotic/examples/example-single.sto
src/easel/demotic/examples/example.fa
src/easel/demotic/examples/example.fasta.out
src/easel/demotic/examples/example.h2.out
src/easel/demotic/examples/example.hmm
src/easel/demotic/examples/example.hmm2
src/easel/demotic/examples/example.hmmsearch.out
src/easel/demotic/examples/example.ncbi-blastp.out
src/easel/demotic/examples/example.phmmer.out
src/easel/demotic/examples/example.psiblast.out
src/easel/demotic/examples/example.ssearch.out
src/easel/demotic/examples/example.sto
src/easel/demotic/examples/example.wu-blastp.out
src/easel/demotic/fasta2profmark
src/easel/demotic/fasta2tbl
src/easel/demotic/h22profmark
src/easel/demotic/h22tbl
src/easel/demotic/hmmer2profmark
src/easel/demotic/hmmer2tbl
src/easel/demotic/infernal_tab2gff.pl
src/easel/demotic/regress/fasta-profmark.out
src/easel/demotic/regress/fasta-tbl.out
src/easel/demotic/regress/h2-profmark.out
src/easel/demotic/regress/h2-tbl.out
src/easel/demotic/regress/hmmsearch-profmark.out
src/easel/demotic/regress/hmmsearch-tbl.out
src/easel/demotic/regress/ncbi-blastp-profmark.out
src/easel/demotic/regress/ncbi-blastp-tbl.out
src/easel/demotic/regress/phmmer-profmark.out
src/easel/demotic/regress/phmmer-tbl.out
src/easel/demotic/regress/psiblast-profmark.out
src/easel/demotic/regress/psiblast-tbl.out
src/easel/demotic/regress/ssearch-profmark.out
src/easel/demotic/regress/ssearch-tbl.out
src/easel/demotic/regress/wu-blastp-profmark.out
src/easel/demotic/regress/wu-blastp-tbl.out
src/easel/demotic/test.pl
src/easel/devkit/00README
src/easel/devkit/autodoc
src/easel/devkit/c2optlist
src/easel/devkit/cexcerpt
src/easel/devkit/cexcerpt.man
src/easel/devkit/ctags-fix
src/easel/devkit/esl-dependencies
src/easel/devkit/man2optlist
src/easel/devkit/rmanprocess.pl
src/easel/devkit/sedition
src/easel/devkit/sedition-pp
src/easel/devkit/sqc
src/easel/documentation/codestyle.tex
src/easel/documentation/copyright.tex
src/easel/documentation/doctricks.tex
src/easel/documentation/figures/evd_basic.pdf
src/easel/documentation/figures/evd_location.pdf
src/easel/documentation/figures/evd_scale.pdf
src/easel/documentation/figures/gev_density.pdf
src/easel/documentation/figures/gev_logdensity.pdf
src/easel/documentation/figures/rna_elements.ai
src/easel/documentation/figures/rna_elements.eps
src/easel/documentation/figures/rna_elements.pdf
src/easel/documentation/figures/rnaseP-bsu-alignment.ai
src/easel/documentation/figures/rnaseP-bsu-alignment.eps
src/easel/documentation/figures/rnaseP-bsu-alignment.pdf
src/easel/documentation/figures/rnaseP-ecoli.ai
src/easel/documentation/figures/rnaseP-ecoli.eps
src/easel/documentation/figures/rnaseP-ecoli.pdf
src/easel/documentation/format_a2m.tex
src/easel/documentation/format_ncbi.tex
src/easel/documentation/format_stockholm.tex
src/easel/documentation/format_wuss.tex
src/easel/documentation/install.tex
src/easel/documentation/installation.tex
src/easel/documentation/intro.tex
src/easel/documentation/macros.tex
src/easel/documentation/main.tex
src/easel/documentation/Makefile.in
src/easel/documentation/statistics.tex
src/easel/documentation/titlepage.tex
src/easel/documentation/typography.tex
src/easel/easel.c
src/easel/easel.h
src/easel/easel.tex
src/easel/esl_alphabet.c
src/easel/esl_alphabet.h
src/easel/esl_alphabet.tex
src/easel/esl_buffer.c
src/easel/esl_buffer.h
src/easel/esl_buffer.tex
src/easel/esl_cluster.c
src/easel/esl_cluster.h
src/easel/esl_cluster.tex
src/easel/esl_composition.c
src/easel/esl_composition.h
src/easel/esl_config.h.in
src/easel/esl_dirichlet.c
src/easel/esl_dirichlet.h
src/easel/esl_dirichlet.tex
src/easel/esl_distance.c
src/easel/esl_distance.h
src/easel/esl_distance.tex
src/easel/esl_dmatrix.c
src/easel/esl_dmatrix.h
src/easel/esl_dmatrix.tex
src/easel/esl_exponential.c
src/easel/esl_exponential.h
src/easel/esl_exponential.tex
src/easel/esl_fileparser.c
src/easel/esl_fileparser.h
src/easel/esl_fileparser.tex
src/easel/esl_gamma.c
src/easel/esl_gamma.h
src/easel/esl_gamma.tex
src/easel/esl_getopts.c
src/easel/esl_getopts.h
src/easel/esl_getopts.tex
src/easel/esl_gev.c
src/easel/esl_gev.h
src/easel/esl_gev.tex
src/easel/esl_gumbel.c
src/easel/esl_gumbel.h
src/easel/esl_gumbel.tex
src/easel/esl_histogram.c
src/easel/esl_histogram.h
src/easel/esl_histogram.tex
src/easel/esl_hmm.c
src/easel/esl_hmm.h
src/easel/esl_hyperexp.c
src/easel/esl_hyperexp.h
src/easel/esl_hyperexp.tex
src/easel/esl_keyhash.c
src/easel/esl_keyhash.h
src/easel/esl_keyhash.tex
src/easel/esl_mem.c
src/easel/esl_mem.h
src/easel/esl_minimizer.c
src/easel/esl_minimizer.h
src/easel/esl_minimizer.tex
src/easel/esl_mixgev.c
src/easel/esl_mixgev.h
src/easel/esl_mpi.c
src/easel/esl_mpi.h
src/easel/esl_mpi.tex
src/easel/esl_msa.c
src/easel/esl_msa.h
src/easel/esl_msa.tex
src/easel/esl_msa_testfiles/selex/00MANIFEST
src/easel/esl_msa_testfiles/selex/selex.bad.1
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src/easel/esl_msa_testfiles/selex/selex.good.1
src/easel/esl_msa_testfiles/selex/selex.good.2
src/easel/esl_msa_testfiles/selex/selex.good.3
src/easel/esl_msacluster.c
src/easel/esl_msacluster.h
src/easel/esl_msacluster.tex
src/easel/esl_msafile.c
src/easel/esl_msafile.h
src/easel/esl_msafile2.c
src/easel/esl_msafile2.h
src/easel/esl_msafile_a2m.c
src/easel/esl_msafile_a2m.h
src/easel/esl_msafile_afa.c
src/easel/esl_msafile_afa.h
src/easel/esl_msafile_clustal.c
src/easel/esl_msafile_clustal.h
src/easel/esl_msafile_phylip.c
src/easel/esl_msafile_phylip.h
src/easel/esl_msafile_psiblast.c
src/easel/esl_msafile_psiblast.h
src/easel/esl_msafile_selex.c
src/easel/esl_msafile_selex.h
src/easel/esl_msafile_stockholm.c
src/easel/esl_msafile_stockholm.h
src/easel/esl_msashuffle.c
src/easel/esl_msashuffle.h
src/easel/esl_msaweight.c
src/easel/esl_msaweight.h
src/easel/esl_msaweight.tex
src/easel/esl_normal.c
src/easel/esl_normal.h
src/easel/esl_normal.tex
src/easel/esl_paml.c
src/easel/esl_paml.h
src/easel/esl_paml.tex
src/easel/esl_random.c
src/easel/esl_random.h
src/easel/esl_random.tex
src/easel/esl_randomseq.c
src/easel/esl_randomseq.h
src/easel/esl_randomseq.tex
src/easel/esl_ratematrix.c
src/easel/esl_ratematrix.h
src/easel/esl_ratematrix.tex
src/easel/esl_recorder.c
src/easel/esl_recorder.h
src/easel/esl_regexp.c
src/easel/esl_regexp.h
src/easel/esl_regexp.tex
src/easel/esl_rootfinder.c
src/easel/esl_rootfinder.h
src/easel/esl_rootfinder.tex
src/easel/esl_scorematrix.c
src/easel/esl_scorematrix.h
src/easel/esl_scorematrix.tex
src/easel/esl_sq.c
src/easel/esl_sq.h
src/easel/esl_sq.tex
src/easel/esl_sqio.c
src/easel/esl_sqio.h
src/easel/esl_sqio.tex
src/easel/esl_sqio_ascii.c
src/easel/esl_sqio_ascii.h
src/easel/esl_sqio_ncbi.c
src/easel/esl_sqio_ncbi.h
src/easel/esl_sse.c
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src/easel/esl_sse.tex
src/easel/esl_ssi.c
src/easel/esl_ssi.h
src/easel/esl_ssi.tex
src/easel/esl_stack.c
src/easel/esl_stack.h
src/easel/esl_stack.tex
src/easel/esl_stats.c
src/easel/esl_stats.h
src/easel/esl_stats.tex
src/easel/esl_stopwatch.c
src/easel/esl_stopwatch.h
src/easel/esl_stopwatch.tex
src/easel/esl_stretchexp.c
src/easel/esl_stretchexp.h
src/easel/esl_stretchexp.tex
src/easel/esl_swat.c
src/easel/esl_swat.tex
src/easel/esl_threads.c
src/easel/esl_threads.h
src/easel/esl_translate.c
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src/easel/esl_tree.c
src/easel/esl_tree.h
src/easel/esl_tree.tex
src/easel/esl_vectorops.c
src/easel/esl_vectorops.h
src/easel/esl_vectorops.tex
src/easel/esl_vmx.c
src/easel/esl_vmx.h
src/easel/esl_weibull.c
src/easel/esl_weibull.h
src/easel/esl_weibull.tex
src/easel/esl_workqueue.c
src/easel/esl_workqueue.h
src/easel/esl_wuss.c
src/easel/esl_wuss.h
src/easel/esl_wuss.tex
src/easel/formats/BLOSUM62
src/easel/formats/embl
src/easel/formats/fasta
src/easel/formats/fasta.2
src/easel/formats/fasta.bad.1
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src/easel/formats/fasta.bad.3
src/easel/formats/fasta.odd.1
src/easel/formats/genbank
src/easel/formats/genbank.2
src/easel/formats/genbank.bad.1
src/easel/formats/stockholm.1
src/easel/formats/uniprot
src/easel/formats/wag.dat
src/easel/INSTALL
src/easel/install-sh
src/easel/interface_gsl.c
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src/easel/interface_lapack.c
src/easel/interface_lapack.h
src/easel/LICENSE
src/easel/LICENSE.sh.in
src/easel/LICENSE.tag
src/easel/Makefile.in
src/easel/miniapps/esl-afetch.c
src/easel/miniapps/esl-afetch.itest.pl
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src/easel/miniapps/esl-alimanip.c
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