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Sequence analysis library used by Eddy/Rivas lab code
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demotic Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
devkit
documentation Overhauls how 'make install' works. Apr 3, 2018
esl_msa_testfiles Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
formats Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
m4 Adds detection and support for "SSE4" vs. "SSE" vector implementations. Jun 6, 2018
miniapps Fixes for HMMER #141 and #120: compile fails on i586, ppc64be. Jun 9, 2018
testsuite Fixes for HMMER #141 and #120: compile fails on i586, ppc64be. Jun 9, 2018
.gitignore Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
LICENSE Removes outdated 00CHECKLIST, and INSTALL. May 30, 2018
Makefile.in Adds SSE4_CFLAGS in Makefile.in to fix iss#28. Apr 22, 2019
README.md Removes outdated 00CHECKLIST, and INSTALL. May 30, 2018
config.guess Overhauls how 'make install' works. Apr 3, 2018
config.sub Overhauls how 'make install' works. Apr 3, 2018
configure.ac Updates versioning to 0.45h. Jun 11, 2018
decoy_config.h.in Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
easel.c Removes/cleans some cruft about daemon format. Jun 2, 2018
easel.h Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
easel.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_alloc.c
esl_alloc.h Adds esl_alloc: portable aligned memory allocation. Feb 10, 2017
esl_alloc.md Documents esl_alloc benchmarking (in esl_alloc.md) Feb 12, 2017
esl_alphabet.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_alphabet.h
esl_alphabet.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_arr2.c
esl_arr2.h Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_arr3.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_arr3.h Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_avx.c esl_neon64 deleted. ARM NEON code is unified in esl_neon. May 25, 2017
esl_avx.h Fixes some casting issues in AVX-512 code. Jun 5, 2017
esl_avx512.c Missing stdio.h header in avx512 empty-compile-unit silencing. Jun 2, 2017
esl_avx512.h
esl_buffer.c fixes intermittent glitch in esl_buffer_utest detected by valgrind Jun 4, 2018
esl_buffer.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_buffer.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_cluster.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_cluster.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_cluster.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_composition.c Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_composition.h Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_config.h.in
esl_cpu.c Adds detection and support for "SSE4" vs. "SSE" vector implementations. Jun 6, 2018
esl_cpu.h Adds detection and support for "SSE4" vs. "SSE" vector implementations. Jun 6, 2018
esl_dirichlet.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_dirichlet.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_dirichlet.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_distance.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_distance.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_distance.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_dmatrix.c
esl_dmatrix.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_dmatrix.tex
esl_dsqdata.c Fixes gcc-8 compiler warnings in esl_dsqdata utest snprintf()'s. Jun 1, 2018
esl_dsqdata.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_dsqdata.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_exponential.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_exponential.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_exponential.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_fileparser.c Fixes compiler warnings (gcc7, Linux) Feb 22, 2018
esl_fileparser.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_fileparser.tex
esl_gamma.c
esl_gamma.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_gamma.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_gencode.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_gencode.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_getopts.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_getopts.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_getopts.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_gev.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_gev.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_gev.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_gumbel.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_gumbel.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_gumbel.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_heap.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_heap.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_histogram.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_histogram.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_histogram.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_hmm.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_hmm.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_huffman.c Appeasement of new gcc6 --Wmisleading-indentation warning. Jun 1, 2017
esl_huffman.h Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_hyperexp.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_hyperexp.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_hyperexp.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_keyhash.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_keyhash.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_keyhash.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_mem.c
esl_mem.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_minimizer.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_minimizer.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_minimizer.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_mixgev.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_mixgev.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_mpi.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_mpi.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_mpi.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_msa.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_msa.h
esl_msa.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_msacluster.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msacluster.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msacluster.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_msafile.c Updates man pages and man->tex conversion; adds rmanprocess.py May 1, 2018
esl_msafile.h
esl_msafile.md Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_msafile2.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_msafile2.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_a2m.c Clarifies A2M format parse error message when illegal 'O' may be pres… Jul 12, 2017
esl_msafile_a2m.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_afa.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_afa.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_clustal.c Appeasement of new gcc6 --Wmisleading-indentation warning. Jun 1, 2017
esl_msafile_clustal.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_phylip.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_phylip.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_psiblast.c Appeasement of new gcc6 --Wmisleading-indentation warning. Jun 1, 2017
esl_msafile_psiblast.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_selex.c
esl_msafile_selex.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_stockholm.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msafile_stockholm.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msashuffle.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msashuffle.h
esl_msaweight.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msaweight.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_msaweight.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_neon.c
esl_neon.h Renamed left,right shift functions in esl_avx for consistency. Jun 4, 2017
esl_normal.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_normal.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_normal.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_paml.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_paml.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_paml.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_quicksort.c
esl_quicksort.h
esl_random.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_random.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_random.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_randomseq.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_randomseq.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_randomseq.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_ratematrix.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_ratematrix.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_ratematrix.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_recorder.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_recorder.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_red_black.c Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_red_black.h Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_regexp.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_regexp.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_regexp.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_rootfinder.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_rootfinder.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_rootfinder.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_scorematrix.c Documents source of the "DNA1" score matrix from Travis. Aug 22, 2017
esl_scorematrix.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_scorematrix.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_sq.c Appeasement of new gcc6 --Wmisleading-indentation warning. Jun 1, 2017
esl_sq.h
esl_sq.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_sqio.c Updates man pages and man->tex conversion; adds rmanprocess.py May 1, 2018
esl_sqio.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_sqio.tex Removes easel's "augmentation" concept; adds safety from gnu autoheader. Apr 28, 2017
esl_sqio_ascii.c Removes/cleans some cruft about daemon format. Jun 2, 2018
esl_sqio_ascii.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_sqio_ncbi.c Small tweaks made when removing HMMER3 dummy implementation. Jun 4, 2018
esl_sqio_ncbi.h
esl_sse.c Adds detection and support for "SSE4" vs. "SSE" vector implementations. Jun 6, 2018
esl_sse.h Adds detection and support for "SSE4" vs. "SSE" vector implementations. Jun 6, 2018
esl_sse.tex Adds esl_sse_hmax_epi8(); SSE now requires SSE4.1 May 18, 2017
esl_ssi.c Small tweaks made when removing HMMER3 dummy implementation. Jun 4, 2018
esl_ssi.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_ssi.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_stack.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stack.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stack.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_stats.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_stats.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stats.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_stopwatch.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stopwatch.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stopwatch.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_stretchexp.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stretchexp.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_stretchexp.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_swat.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_swat.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_threads.c Adds esl_threads_GetCPUCount(). Aug 21, 2017
esl_threads.h Adds esl_threads_GetCPUCount(). Aug 21, 2017
esl_tree.c Adds esl_arr2, esl_arr3, deprecating esl_Free2D(), esl_Free3D(). Feb 2, 2018
esl_tree.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_tree.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_vectorops.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_vectorops.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_vectorops.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_vmx.c Adds detection and support for "SSE4" vs. "SSE" vector implementations. Jun 6, 2018
esl_vmx.h Changes for POWER compatibility Jun 16, 2017
esl_weibull.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_weibull.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_weibull.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
esl_workqueue.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_workqueue.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_wuss.c Additional changes during vectorconf upgrade of HMMER, Infernal. Jan 31, 2017
esl_wuss.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
esl_wuss.tex Revert "Added a basic red-black tree implementation to easel" Feb 28, 2017
install-sh fixing permission problems Jun 17, 2016
interface_gsl.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
interface_gsl.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
interface_lapack.c Merge branch 'develop' back into vectorconf. Apr 29, 2017
interface_lapack.h Merge branch 'develop' back into vectorconf. Apr 29, 2017
makeTAGS.sh Overhauls how 'make install' works. Apr 3, 2018

README.md

Easel - a library of C functions for biological sequence analysis

Easel is an ANSI C code library developed by the Eddy/Rivas laboratory at Harvard for computational analysis of biological sequences using probabilistic models. Easel is used by HMMER, the profile hidden Markov model software that underlies several protein and DNA sequence family databases such as Pfam, and by Infernal, the profile stochastic context-free grammar software that underlies the Rfam RNA family database. Easel aims to make similar applications more robust and easier to develop, by providing a set of reusable, documented, and well-tested functions.

Easel is not (yet) released on its own. It is part of the HMMER and Infernal releases.

To participate in Easel development, visit us at github.

to clone a copy of Easel source from github:

    % git clone https://github.com/EddyRivasLab/easel
    % cd easel
    % autoconf

and to build:

   % ./configure
   % make

and to test:

   % make check
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