bin/alimask
bin/easel
bin/esl-afetch
bin/esl-alimanip
bin/esl-alimap
bin/esl-alimask
bin/esl-alimerge
bin/esl-alipid
bin/esl-alirev
bin/esl-alistat
bin/esl-compalign
bin/esl-compstruct
bin/esl-construct
bin/esl-histplot
bin/esl-mask
bin/esl-mixdchlet
bin/esl-reformat
bin/esl-selectn
bin/esl-seqrange
bin/esl-seqstat
bin/esl-sfetch
bin/esl-shuffle
bin/esl-ssdraw
bin/esl-translate
bin/esl-weight
bin/hmmalign
bin/hmmbuild
bin/hmmconvert
bin/hmmemit
bin/hmmfetch
bin/hmmlogo
bin/hmmpgmd
bin/hmmpgmd_shard
bin/hmmpress
bin/hmmscan
bin/hmmsearch
bin/hmmsim
bin/hmmstat
bin/jackhmmer
bin/makehmmerdb
bin/nhmmer
bin/nhmmscan
bin/phmmer
share/easel/.gitignore
share/easel/.travis.yml
share/easel/LICENSE
share/easel/Makefile
share/easel/Makefile.in
share/easel/README.md
share/easel/config.guess
share/easel/config.sub
share/easel/configure.ac
share/easel/decoy_config.h
share/easel/decoy_config.h.in
share/easel/demotic/00README
share/easel/demotic/blast2profmark
share/easel/demotic/blast2tbl
share/easel/demotic/demotic_blast.pm
share/easel/demotic/demotic_fasta.pm
share/easel/demotic/demotic_h2.pm
share/easel/demotic/demotic_hmmer.pm
share/easel/demotic/demotic_infernal_tab.pm
share/easel/demotic/examples/example-single-psiquery.fa
share/easel/demotic/examples/example-single.asnt
share/easel/demotic/examples/example-single.fa
share/easel/demotic/examples/example-single.fa.phr
share/easel/demotic/examples/example-single.fa.pin
share/easel/demotic/examples/example-single.fa.psq
share/easel/demotic/examples/example-single.pbl
share/easel/demotic/examples/example-single.sto
share/easel/demotic/examples/example.fa
share/easel/demotic/examples/example.fasta.out
share/easel/demotic/examples/example.h2.out
share/easel/demotic/examples/example.hmm
share/easel/demotic/examples/example.hmm2
share/easel/demotic/examples/example.hmmsearch.out
share/easel/demotic/examples/example.ncbi-blastp.out
share/easel/demotic/examples/example.phmmer.out
share/easel/demotic/examples/example.psiblast.out
share/easel/demotic/examples/example.ssearch.out
share/easel/demotic/examples/example.sto
share/easel/demotic/examples/example.wu-blastp.out
share/easel/demotic/fasta2profmark
share/easel/demotic/fasta2tbl
share/easel/demotic/h22profmark
share/easel/demotic/h22tbl
share/easel/demotic/hmmer2profmark
share/easel/demotic/hmmer2tbl
share/easel/demotic/infernal_tab2gff.pl
share/easel/demotic/regress/fasta-profmark.out
share/easel/demotic/regress/fasta-tbl.out
share/easel/demotic/regress/h2-profmark.out
share/easel/demotic/regress/h2-tbl.out
share/easel/demotic/regress/hmmsearch-profmark.out
share/easel/demotic/regress/hmmsearch-tbl.out
share/easel/demotic/regress/ncbi-blastp-profmark.out
share/easel/demotic/regress/ncbi-blastp-tbl.out
share/easel/demotic/regress/phmmer-profmark.out
share/easel/demotic/regress/phmmer-tbl.out
share/easel/demotic/regress/psiblast-profmark.out
share/easel/demotic/regress/psiblast-tbl.out
share/easel/demotic/regress/ssearch-profmark.out
share/easel/demotic/regress/ssearch-tbl.out
share/easel/demotic/regress/wu-blastp-profmark.out
share/easel/demotic/regress/wu-blastp-tbl.out
share/easel/demotic/test.pl
share/easel/devkit/00README
share/easel/devkit/autodoc
share/easel/devkit/autodoc.md
share/easel/devkit/autodoc.py
share/easel/devkit/c2optlist
share/easel/devkit/cexcerpt
share/easel/devkit/cexcerpt.man
share/easel/devkit/ctags-fix
share/easel/devkit/man2optlist
share/easel/devkit/rmanprocess.pl
share/easel/devkit/rmanprocess.py
share/easel/devkit/sedition
share/easel/devkit/sedition-pp
share/easel/devkit/sqc
share/easel/devkit/techtree.py
share/easel/documentation/Makefile
share/easel/documentation/Makefile.in
share/easel/documentation/codestyle.md
share/easel/documentation/codestyle.tex
share/easel/documentation/copyright.tex
share/easel/documentation/doctricks.tex
share/easel/documentation/figures/easel_techtree.ai
share/easel/documentation/figures/easel_techtree.pdf
share/easel/documentation/figures/easel_techtree.png
share/easel/documentation/figures/evd_basic.pdf
share/easel/documentation/figures/evd_location.pdf
share/easel/documentation/figures/evd_scale.pdf
share/easel/documentation/figures/gev_density.pdf
share/easel/documentation/figures/gev_logdensity.pdf
share/easel/documentation/figures/rna_elements.ai
share/easel/documentation/figures/rna_elements.eps
share/easel/documentation/figures/rna_elements.pdf
share/easel/documentation/figures/rnaseP-bsu-alignment.ai
share/easel/documentation/figures/rnaseP-bsu-alignment.eps
share/easel/documentation/figures/rnaseP-bsu-alignment.pdf
share/easel/documentation/figures/rnaseP-ecoli.ai
share/easel/documentation/figures/rnaseP-ecoli.eps
share/easel/documentation/figures/rnaseP-ecoli.pdf
share/easel/documentation/format_a2m.tex
share/easel/documentation/format_ncbi.tex
share/easel/documentation/format_stockholm.tex
share/easel/documentation/format_wuss.tex
share/easel/documentation/install.tex
share/easel/documentation/installation.tex
share/easel/documentation/intro.tex
share/easel/documentation/macros.tex
share/easel/documentation/main.tex
share/easel/documentation/statistics.tex
share/easel/documentation/titlepage.tex
share/easel/documentation/typography.tex
share/easel/easel.c
share/easel/easel.h
share/easel/easel.o
share/easel/easel.tex
share/easel/esl_alloc.c
share/easel/esl_alloc.h
share/easel/esl_alloc.md
share/easel/esl_alloc.o
share/easel/esl_alphabet.c
share/easel/esl_alphabet.h
share/easel/esl_alphabet.o
share/easel/esl_alphabet.tex
share/easel/esl_arr2.c
share/easel/esl_arr2.h
share/easel/esl_arr2.o
share/easel/esl_arr3.c
share/easel/esl_arr3.h
share/easel/esl_arr3.o
share/easel/esl_avx.c
share/easel/esl_avx.h
share/easel/esl_avx.o
share/easel/esl_avx512.c
share/easel/esl_avx512.h
share/easel/esl_avx512.o
share/easel/esl_bitfield.c
share/easel/esl_bitfield.h
share/easel/esl_bitfield.o
share/easel/esl_buffer.c
share/easel/esl_buffer.h
share/easel/esl_buffer.o
share/easel/esl_buffer.tex
share/easel/esl_cluster.c
share/easel/esl_cluster.h
share/easel/esl_cluster.o
share/easel/esl_cluster.tex
share/easel/esl_composition.c
share/easel/esl_composition.h
share/easel/esl_composition.o
share/easel/esl_config.h
share/easel/esl_config.h.in
share/easel/esl_cpu.c
share/easel/esl_cpu.h
share/easel/esl_cpu.o
share/easel/esl_dirichlet.c
share/easel/esl_dirichlet.h
share/easel/esl_dirichlet.o
share/easel/esl_dirichlet.tex
share/easel/esl_distance.c
share/easel/esl_distance.h
share/easel/esl_distance.o
share/easel/esl_distance.tex
share/easel/esl_dmatrix.c
share/easel/esl_dmatrix.h
share/easel/esl_dmatrix.o
share/easel/esl_dmatrix.tex
share/easel/esl_dsqdata.c
share/easel/esl_dsqdata.h
share/easel/esl_dsqdata.md
share/easel/esl_dsqdata.o
share/easel/esl_dsqdata.tex
share/easel/esl_exponential.c
share/easel/esl_exponential.h
share/easel/esl_exponential.o
share/easel/esl_exponential.tex
share/easel/esl_fileparser.c
share/easel/esl_fileparser.h
share/easel/esl_fileparser.o
share/easel/esl_fileparser.tex
share/easel/esl_gamma.c
share/easel/esl_gamma.h
share/easel/esl_gamma.o
share/easel/esl_gamma.tex
share/easel/esl_gencode.c
share/easel/esl_gencode.h
share/easel/esl_gencode.o
share/easel/esl_getopts.c
share/easel/esl_getopts.h
share/easel/esl_getopts.md
share/easel/esl_getopts.o
share/easel/esl_gev.c
share/easel/esl_gev.h
share/easel/esl_gev.o
share/easel/esl_gev.tex
share/easel/esl_graph.c
share/easel/esl_graph.h
share/easel/esl_graph.o
share/easel/esl_gumbel.c
share/easel/esl_gumbel.h
share/easel/esl_gumbel.o
share/easel/esl_gumbel.tex
share/easel/esl_heap.c
share/easel/esl_heap.h
share/easel/esl_heap.o
share/easel/esl_histogram.c
share/easel/esl_histogram.h
share/easel/esl_histogram.o
share/easel/esl_histogram.tex
share/easel/esl_hmm.c
share/easel/esl_hmm.h
share/easel/esl_hmm.o
share/easel/esl_huffman.c
share/easel/esl_huffman.h
share/easel/esl_huffman.o
share/easel/esl_hyperexp.c
share/easel/esl_hyperexp.h
share/easel/esl_hyperexp.o
share/easel/esl_hyperexp.tex
share/easel/esl_json.c
share/easel/esl_json.h
share/easel/esl_json.o
share/easel/esl_keyhash.c
share/easel/esl_keyhash.h
share/easel/esl_keyhash.o
share/easel/esl_keyhash.tex
share/easel/esl_matrixops.c
share/easel/esl_matrixops.h
share/easel/esl_matrixops.o
share/easel/esl_mem.c
share/easel/esl_mem.h
share/easel/esl_mem.md
share/easel/esl_mem.o
share/easel/esl_minimizer.c
share/easel/esl_minimizer.h
share/easel/esl_minimizer.o
share/easel/esl_minimizer.tex
share/easel/esl_mixdchlet.c
share/easel/esl_mixdchlet.h
share/easel/esl_mixdchlet.o
share/easel/esl_mixdchlet.tex
share/easel/esl_mixgev.c
share/easel/esl_mixgev.h
share/easel/esl_mixgev.o
share/easel/esl_mpi.c
share/easel/esl_mpi.h
share/easel/esl_mpi.o
share/easel/esl_mpi.tex
share/easel/esl_msa.c
share/easel/esl_msa.h
share/easel/esl_msa.o
share/easel/esl_msa.tex
share/easel/esl_msa_testfiles/a2m/a2m.good.1
share/easel/esl_msa_testfiles/a2m/a2m.good.2
share/easel/esl_msa_testfiles/afa/afa.good.1
share/easel/esl_msa_testfiles/afa/afa.good.2
share/easel/esl_msa_testfiles/afa/afa.good.3
share/easel/esl_msa_testfiles/clustal/clustal.good.1
share/easel/esl_msa_testfiles/clustal/clustal.good.2
share/easel/esl_msa_testfiles/phylip/phylip.ambig.1
share/easel/esl_msa_testfiles/phylip/phylip.bad.1
share/easel/esl_msa_testfiles/phylip/phylip.bad.10
share/easel/esl_msa_testfiles/phylip/phylip.bad.11
share/easel/esl_msa_testfiles/phylip/phylip.bad.2
share/easel/esl_msa_testfiles/phylip/phylip.bad.3
share/easel/esl_msa_testfiles/phylip/phylip.bad.4
share/easel/esl_msa_testfiles/phylip/phylip.bad.5
share/easel/esl_msa_testfiles/phylip/phylip.bad.6
share/easel/esl_msa_testfiles/phylip/phylip.bad.7
share/easel/esl_msa_testfiles/phylip/phylip.bad.8
share/easel/esl_msa_testfiles/phylip/phylip.bad.9
share/easel/esl_msa_testfiles/phylip/phylip.good.1
share/easel/esl_msa_testfiles/phylip/phylip.good.2
share/easel/esl_msa_testfiles/phylip/phylip.good.3
share/easel/esl_msa_testfiles/phylips/phylips.good.1
share/easel/esl_msa_testfiles/phylips/phylips.good.2
share/easel/esl_msa_testfiles/psiblast/psiblast.good.1
share/easel/esl_msa_testfiles/psiblast/psiblast.good.2
share/easel/esl_msa_testfiles/selex/00MANIFEST
share/easel/esl_msa_testfiles/selex/selex.bad.1
share/easel/esl_msa_testfiles/selex/selex.bad.10
share/easel/esl_msa_testfiles/selex/selex.bad.11
share/easel/esl_msa_testfiles/selex/selex.bad.12
share/easel/esl_msa_testfiles/selex/selex.bad.13
share/easel/esl_msa_testfiles/selex/selex.bad.14
share/easel/esl_msa_testfiles/selex/selex.bad.2
share/easel/esl_msa_testfiles/selex/selex.bad.3
share/easel/esl_msa_testfiles/selex/selex.bad.4
share/easel/esl_msa_testfiles/selex/selex.bad.5
share/easel/esl_msa_testfiles/selex/selex.bad.6
share/easel/esl_msa_testfiles/selex/selex.bad.7
share/easel/esl_msa_testfiles/selex/selex.bad.8
share/easel/esl_msa_testfiles/selex/selex.bad.9
share/easel/esl_msa_testfiles/selex/selex.good.1
share/easel/esl_msa_testfiles/selex/selex.good.2
share/easel/esl_msa_testfiles/selex/selex.good.3
share/easel/esl_msa_testfiles/selex/selex.good.4
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.1
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.2
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.3
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.4
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.5
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.6
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.7
share/easel/esl_msa_testfiles/stockholm/stockholm.bad.8
share/easel/esl_msa_testfiles/stockholm/stockholm.good.1
share/easel/esl_msacluster.c
share/easel/esl_msacluster.h
share/easel/esl_msacluster.o
share/easel/esl_msacluster.tex
share/easel/esl_msafile.c
share/easel/esl_msafile.h
share/easel/esl_msafile.md
share/easel/esl_msafile.o
share/easel/esl_msafile2.c
share/easel/esl_msafile2.h
share/easel/esl_msafile2.o
share/easel/esl_msafile_a2m.c
share/easel/esl_msafile_a2m.h
share/easel/esl_msafile_a2m.o
share/easel/esl_msafile_afa.c
share/easel/esl_msafile_afa.h
share/easel/esl_msafile_afa.o
share/easel/esl_msafile_clustal.c
share/easel/esl_msafile_clustal.h
share/easel/esl_msafile_clustal.o
share/easel/esl_msafile_phylip.c
share/easel/esl_msafile_phylip.h
share/easel/esl_msafile_phylip.o
share/easel/esl_msafile_psiblast.c
share/easel/esl_msafile_psiblast.h
share/easel/esl_msafile_psiblast.o
share/easel/esl_msafile_selex.c
share/easel/esl_msafile_selex.h
share/easel/esl_msafile_selex.o
share/easel/esl_msafile_stockholm.c
share/easel/esl_msafile_stockholm.h
share/easel/esl_msafile_stockholm.o
share/easel/esl_msashuffle.c
share/easel/esl_msashuffle.h
share/easel/esl_msashuffle.o
share/easel/esl_msaweight.c
share/easel/esl_msaweight.h
share/easel/esl_msaweight.md
share/easel/esl_msaweight.o
share/easel/esl_msaweight.tex
share/easel/esl_neon.c
share/easel/esl_neon.h
share/easel/esl_neon.o
share/easel/esl_normal.c
share/easel/esl_normal.h
share/easel/esl_normal.o
share/easel/esl_normal.tex
share/easel/esl_paml.c
share/easel/esl_paml.h
share/easel/esl_paml.o
share/easel/esl_paml.tex
share/easel/esl_quicksort.c
share/easel/esl_quicksort.h
share/easel/esl_quicksort.o
share/easel/esl_rand64.c
share/easel/esl_rand64.h
share/easel/esl_rand64.o
share/easel/esl_random.c
share/easel/esl_random.h
share/easel/esl_random.o
share/easel/esl_random.tex
share/easel/esl_randomseq.c
share/easel/esl_randomseq.h
share/easel/esl_randomseq.o
share/easel/esl_randomseq.tex
share/easel/esl_ratematrix.c
share/easel/esl_ratematrix.h
share/easel/esl_ratematrix.o
share/easel/esl_ratematrix.tex
share/easel/esl_recorder.c
share/easel/esl_recorder.h
share/easel/esl_recorder.o
share/easel/esl_red_black.c
share/easel/esl_red_black.h
share/easel/esl_red_black.o
share/easel/esl_regexp.c
share/easel/esl_regexp.h
share/easel/esl_regexp.md
share/easel/esl_regexp.o
share/easel/esl_regexp.tex
share/easel/esl_rootfinder.c
share/easel/esl_rootfinder.h
share/easel/esl_rootfinder.o
share/easel/esl_rootfinder.tex
share/easel/esl_scorematrix.c
share/easel/esl_scorematrix.h
share/easel/esl_scorematrix.o
share/easel/esl_scorematrix.tex
share/easel/esl_sq.c
share/easel/esl_sq.h
share/easel/esl_sq.o
share/easel/esl_sq.tex
share/easel/esl_sqio.c
share/easel/esl_sqio.h
share/easel/esl_sqio.o
share/easel/esl_sqio.tex
share/easel/esl_sqio_ascii.c
share/easel/esl_sqio_ascii.h
share/easel/esl_sqio_ascii.o
share/easel/esl_sqio_ncbi.c
share/easel/esl_sqio_ncbi.h
share/easel/esl_sqio_ncbi.o
share/easel/esl_sse.c
share/easel/esl_sse.h
share/easel/esl_sse.o
share/easel/esl_sse.tex
share/easel/esl_ssi.c
share/easel/esl_ssi.h
share/easel/esl_ssi.o
share/easel/esl_ssi.tex
share/easel/esl_stack.c
share/easel/esl_stack.h
share/easel/esl_stack.o
share/easel/esl_stack.tex
share/easel/esl_stats.c
share/easel/esl_stats.h
share/easel/esl_stats.o
share/easel/esl_stats.tex
share/easel/esl_stopwatch.c
share/easel/esl_stopwatch.h
share/easel/esl_stopwatch.o
share/easel/esl_stopwatch.tex
share/easel/esl_stretchexp.c
share/easel/esl_stretchexp.h
share/easel/esl_stretchexp.o
share/easel/esl_stretchexp.tex
share/easel/esl_subcmd.c
share/easel/esl_subcmd.h
share/easel/esl_subcmd.o
share/easel/esl_swat.c
share/easel/esl_swat.tex
share/easel/esl_threads.c
share/easel/esl_threads.h
share/easel/esl_threads.o
share/easel/esl_tree.c
share/easel/esl_tree.h
share/easel/esl_tree.o
share/easel/esl_tree.tex
share/easel/esl_varint.c
share/easel/esl_varint.h
share/easel/esl_varint.md
share/easel/esl_varint.o
share/easel/esl_vectorops.c
share/easel/esl_vectorops.h
share/easel/esl_vectorops.md
share/easel/esl_vectorops.o
share/easel/esl_vmx.c
share/easel/esl_vmx.h
share/easel/esl_vmx.o
share/easel/esl_weibull.c
share/easel/esl_weibull.h
share/easel/esl_weibull.o
share/easel/esl_weibull.tex
share/easel/esl_workqueue.c
share/easel/esl_workqueue.h
share/easel/esl_workqueue.o
share/easel/esl_wuss.c
share/easel/esl_wuss.h
share/easel/esl_wuss.o
share/easel/esl_wuss.tex
share/easel/formats/BLOSUM62
share/easel/formats/embl
share/easel/formats/fasta
share/easel/formats/fasta.2
share/easel/formats/fasta.bad.1
share/easel/formats/fasta.bad.2
share/easel/formats/fasta.bad.3
share/easel/formats/fasta.odd.1
share/easel/formats/genbank
share/easel/formats/genbank.2
share/easel/formats/genbank.bad.1
share/easel/formats/stockholm.1
share/easel/formats/uniprot
share/easel/formats/wag.dat
share/easel/install-sh
share/easel/interface_gsl.c
share/easel/interface_gsl.h
share/easel/interface_lapack.c
share/easel/interface_lapack.h
share/easel/libeasel.a
share/easel/m4/ax_check_compile_flag.m4
share/easel/m4/ax_check_gnu_make.m4
share/easel/m4/ax_compiler_vendor.m4
share/easel/m4/ax_gcc_func_attribute.m4
share/easel/m4/ax_prog_cc_mpi.m4
share/easel/m4/ax_pthread.m4
share/easel/m4/esl_avx.m4
share/easel/m4/esl_avx512.m4
share/easel/m4/esl_cuda.m4
share/easel/m4/esl_neon.m4
share/easel/m4/esl_pic_flags.m4
share/easel/m4/esl_sse.m4
share/easel/m4/esl_sse4.m4
share/easel/m4/esl_vmx.m4
share/easel/makeTAGS.sh
share/easel/release-notes/RELEASE-0.46.md
share/easel/release-notes/RELEASE-0.47.md
share/easel/release-notes/RELEASE-0.48.md
share/easel/testsuite/Makefile
share/easel/testsuite/Makefile.in
share/easel/testsuite/coverage_report.pl
share/easel/testsuite/e2.sh
share/easel/testsuite/i1-degen-residues.pl
share/easel/testsuite/i2-ncbi-indices.pl
share/easel/testsuite/i3-blank-gf.pl
share/easel/testsuite/parse_test_results.py
share/easel/testsuite/testsuite.sqc
share/easel/testsuite/trna-5.stk
share/easel/testsuite/trna-ssdraw.ps
share/easel/testsuite/valgrind_report.pl
share/man/man1/alimask.1
share/man/man1/esl-afetch.1
share/man/man1/esl-alimanip.1
share/man/man1/esl-alimap.1
share/man/man1/esl-alimask.1
share/man/man1/esl-alimerge.1
share/man/man1/esl-alipid.1
share/man/man1/esl-alirev.1
share/man/man1/esl-alistat.1
share/man/man1/esl-compalign.1
share/man/man1/esl-compstruct.1
share/man/man1/esl-construct.1
share/man/man1/esl-histplot.1
share/man/man1/esl-mask.1
share/man/man1/esl-mixdchlet.1
share/man/man1/esl-reformat.1
share/man/man1/esl-selectn.1
share/man/man1/esl-seqrange.1
share/man/man1/esl-seqstat.1
share/man/man1/esl-sfetch.1
share/man/man1/esl-shuffle.1
share/man/man1/esl-ssdraw.1
share/man/man1/esl-translate.1
share/man/man1/esl-weight.1
share/man/man1/hmmalign.1
share/man/man1/hmmbuild.1
share/man/man1/hmmc2.1
share/man/man1/hmmconvert.1
share/man/man1/hmmemit.1
share/man/man1/hmmer.1
share/man/man1/hmmfetch.1
share/man/man1/hmmlogo.1
share/man/man1/hmmpgmd.1
share/man/man1/hmmpgmd_shard.1
share/man/man1/hmmpress.1
share/man/man1/hmmscan.1
share/man/man1/hmmsearch.1
share/man/man1/hmmsim.1
share/man/man1/hmmstat.1
share/man/man1/jackhmmer.1
share/man/man1/makehmmerdb.1
share/man/man1/nhmmer.1
share/man/man1/nhmmscan.1
share/man/man1/phmmer.1
