Andreas Tille · Andreas Tille · Steffen Möller · Steffen Möller · Steffen Möller · Steffen Möller
--- a/.travis.yml
+++ b/.travis.yml
+language: c
+
+env:
+  - SQC_NONZERO_EXIT=1
+
+script:
+  - git clone -b develop https://github.com/${TRAVIS_REPO_SLUG/hmmer/easel}.git
+  - ln -s easel/aclocal.m4 aclocal.m4
+  - autoconf
+  - ./configure
+  - make
+  - make dev
+  - make check
+
--- a/INSTALL
+++ b/INSTALL
 Brief installation instructions 
-HMMER 3.2.1 (June 2018)
+HMMER 3.3 (Nov 2019)

-Starting from a source distribution, hmmer-3.2.1.tar.gz:
-   uncompress hmmer-3.2.1.tar.gz  
-   tar xf hmmer-3.2.1.tar
-   cd hmmer-3.2.1
+Starting from a source distribution, hmmer-3.3.tar.gz:
+   uncompress hmmer-3.3.tar.gz  
+   tar xf hmmer-3.3.tar
+   cd hmmer-3.3
   ./configure
   make
   make check                        # optional: automated tests

--- a/LICENSE
+++ b/LICENSE
 HMMER - Biological sequence analysis with profile hidden Markov models
-Copyright (C) 1992-2018 Sean R. Eddy
-Copyright (C) 2000-2018 Howard Hughes Medical Institute
-Copyright (C) 2015-2018 President and Fellows of Harvard College
+Copyright (C) 1992-2019 Sean R. Eddy
+Copyright (C) 2000-2019 Howard Hughes Medical Institute
+Copyright (C) 2015-2019 President and Fellows of Harvard College
 Copyright (C) 1992-2004 Washington University School of Medicine
 Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology
 -----------------------------------------------------------------------
@@ -39,12 +39,12 @@ incorporated from other sources, including:
   X Consortium                    

 HMMER uses the Easel software library, which has its own license and
-copyright information. See easel/COPYRIGHT and easel/LICENSE.
+copyright information. See easel/LICENSE.

 HMMER includes patent-pending SIMD technology under a nonexclusive
-license from Michael Farrar. You are sublicensed to use this
-technology specifically for the use, modification, and redistribution
-of HMMER.
+license from the estate of Michael Farrar. You are sublicensed to use
+this technology specifically for the use, modification, and
+redistribution of HMMER.

 HMMER development is supported in part by the National Human Genome
 Research Institute of the US National Institutes of Health under grant

--- a/Makefile.in
+++ b/Makefile.in
@@ -109,6 +109,7 @@ tests:
 # check: Run test suites.
 #
 check:
+	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all	
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
@@ -128,7 +129,7 @@ pdf:
 #          building packages.
 #
 #          Does not use quiet beautification magic; always verbose.
-install: 
+install: all
 	${INSTALL} -d ${DESTDIR}${bindir}
 	${INSTALL} -d ${DESTDIR}${man1dir}
 	${MAKE} -C src install

--- a/README.md
+++ b/README.md
 ## HMMER - biological sequence analysis using profile HMMs

+[![](https://travis-ci.org/EddyRivasLab/hmmer.svg?branch=develop)](https://travis-ci.org/EddyRivasLab/hmmer)
+![](http://img.shields.io/badge/license-BSD-brightgreen.svg)
+
 [HMMER](http://hmmer.org) searches biological sequence databases for
 homologous sequences, using either single sequences or multiple
 sequence alignments as queries. HMMER implements a technology called
@@ -21,7 +24,7 @@ depends on the Easel library, also at
 ```
   % wget http://eddylab.org/software/hmmer/hmmer.tar.gz
   % tar zxf hmmer.tar.gz
-   % cd hmmer-3.2.1
+   % cd hmmer-3.3
   % ./configure --prefix /your/install/path
   % make
   % make check                 # optional: run automated tests
@@ -74,7 +77,9 @@ includes three main branches:

 To build the most recent official release, leave both HMMER and Easel
 on their default **master** branch.  To contribute to HMMER3
-development, you want to be on the **develop** branches.
+development, you want to be on the **develop** branches. If you want
+to send us a pull request on GitHub, please base your changes on our
+**develop** branches.


 ### to report a problem:

--- a/RELEASE-3.2.1
+++ b/RELEASE-3.2.1
-HMMER 3.2.1 release notes    (Jun 2018)
-http://hmmer.org
-
-Release 3.2.1 fixes:
----------------------
-* iss #142: compilation fails ungracefully on unsupported ppc64le
-* iss #140: jackhmmer --fast segfault. Removes --fast 
-  and --symfrac options from jackhmmer and its documentation.
-* iss #141, #120: compilation failures on i586, ppc64be.
-* iss #132: hmmbuild miscounts transitions in final node.
-
-
-
-Release notes for 3.2:
-----------------------
-Larger changes:
-
-* HMMER is now distributed under the BSD license, instead of the GPL.
-
-* The 'make install' has been streamlined. Now we install only
-  programs and man pages, for 18 HMMER programs and 22 Easel miniapps.
-  We don't install development .h headers or .a libraries.
-
-* We changed our default policy on the number of threads/cores that
-  the search programs use. Previously multithreaded programs would use
-  all available cores by default; now we use two worker threads by
-  default (~2 cores), if multiple cores are available. HMMER3 search
-  programs do not scale much beyond 2 cores anyway, due to input
-  saturation and memory use.
-
-* H3 now strictly requires either SSE2 or Altivec/VMX vector
-  support. The portable 'dummy' implementation has been removed. This
-  was an non-vectorized portable pure C implementation, much slower
-  than HMMER3 on x86 and PowerPC platforms with SSE2 or Altivec/VMX
-  vector instructions. We had included it because we could -- HMMER3
-  implements "generic" non-vectorized versions of its core algorithms
-  for unit testing purposes anyway. We thought maybe it'd be useful.
-  As far as I can tell, it was never useful, but several packagers on
-  non-x86, non-PowerPC platforms packaged and distributed it, ignoring
-  the prominent health warnings we put on it.
-
-
-Smaller new features include:
-
-* improved documentation of --mxfile and score matrix file format
-* adds support for EBI's "uncheck all hits" on jackhmmer web site
-* removed experimental hmmbuild --seq_weights_r and --seq_weights_e options
-* appeased new gcc6 --Wmisleading-indentation warning
-* SSI indexing is now robust against duplicate keys
-* autoconf now robust against someone running gnu `autoheader`
-* improved autoconf of SIMD vector support
-* improved autoconf of DAZ,FTZ support on x86 processors
-* improved autodetection of phylip interleaved vs sequential format
-* improved autodetection of A2M vs. aligned FASTA format
-* clarified A2M format parse error when file contains 'O' residue 
-* improved portability to Intel/Solaris
-* FASTA parser now ignores description line after a ctrl-A
-* MSAs output with -A option now include name, acc, desc, author markup.
-* In Easel miniapps, esl-translate replaces previous (buggy) esl-stranslate.
-* Easel miniapps include esl-alirev, reverse complementing RNA/DNA alignment
-* nhmmer/nhmmscan now allow alignments as target dbs
-* target relentropy for DNA models changed from 0.45 to 0.62
-* updated the User Guide
-
-Fixed bugs include:
-
-* nhmmscan faulted on old model files because it expected MAXL field
-* --cut-ga wasn't checking that GA line was actually present in model
-* GA thresholds weren't being captured from DNA/RNA Stockholm alignments
-* A2M alignment parsing was corrupted on lines ending in insertions
-* alphabet-guessing failed for FASTA seq >4096 bytes and <4000 residues
-* genbank to fasta format conversion was leaving extra \n in accession
-* NCBI db format: multithreaded nhmmer was failing to read 
-* NCBI db format: 1st database sequence was skipped for second query (#e6)
-* unit test failures in esl_normal, esl_random due to floating point math
-* nhmmer was corrupted by * symbols in input sequence (iss#118)
-* hmmsearch -A crashed if top-ranked hit has no domains (iss#131)
-* new variety of "backconverted subseq" hmmsearch crash on *'s (iss#135)
-* qsort() callbacks now return -1/0/1 as they should. (Infernal iss#11)
-* esl_buffer hangs when input ends with \r (Easel iss#23) 
-
-For details, you can view and search our issue tracking logs at github:
-  https://github.com/EddyRivasLab/hmmer/issues/   for HMMER itself
-  https://github.com/EddyRivasLab/easel/issues/   for the underlying Easel library
-
-
--- a/RELEASE-3.3.md
+++ b/RELEASE-3.3.md
+# HMMER 3.3 release notes (Nov 2019)
+
+
+## most important changes:
+
+* We improved the `hmmpgmd` search daemon. (`hmmpgmd` is the compute
+  server used at EBI to support their HMMER web servers.)  
+  Now `hmmpgmd` handles large target sequence databases more
+  efficiently by using "sharding". Instead of loading the entire
+  target sequence database into memory on every node, a target
+  database can be sharded across multiple nodes. The `hmmpgmd` daemon
+  also now has its own user guide.
+
+* We improved how we calculate our default sequence weights (Henikoff
+  position-based weights), especially on deep alignments of 10-100K+
+  sequences. Now we calculate PB weights only on consensus columns,
+  not all columns. This avoids some cases of artifactually extreme
+  weights on very gappy alignments. We also changed to a better rule
+  for defining sequence fragments.  These changes give a small
+  improvement in sensitivity/specificity benchmarking of HMMER/Pfam
+  searches, and substantial speed improvements in building profiles on
+  deep alignments. Because of these changes, profile HMMs built with
+  version 3.3 give slightly different scores compared to previous
+  HMMER3 versions.
+
+* Fixed a bug in the `hmmstat` "compKL" (composition KL divergence)
+  calculation, which was off by a constant. Now it is reported as a
+  standard KL divergence in bits.
+
+
+## bug fixes:
+
+* fixed a bug where in some rare and complicated situations, `nhmmer`
+  could report overlapping envelopes on reverse strand. [iss#159]
+
+* Several bugs were fixed in MPI mode, including iss#157 (`hmmsim
+  --mpi` was always segfaulting, even on simple examples) and iss#154
+  (problems in `hmmscan` that were corrupting output data).
+
+* Fixed some 32-bit integer overflow bugs in `hmmpgmd`. 
+
+* Fixed a bug in the `hmmstat` "compKL" (composition KL divergence)
+  calculation, which was off by a constant. Now it is reported as a
+  standard KL divergence in bits.
+
+* Fixed a bug where `hmmconvert --outfmt` wasn't recognizing `3/f` as
+  a format.
+
+
+## Smaller changes
+
+* Our fasta format parser now detects aligned FASTA format (.afa
+  files) more robustly, and will not attempt to read a .afa file as an
+  unaligned sequence file. [iss#153]
+
+* Our `make check` tests depend on Python >= 3.5. Added checks in
+  `./configure` and `make` to fail gracefully if python3 isn't available.
+
+* `./configure` now always calls `AC_PROG_CC_STDC` to add compiler flags
+  for C99 (even with icc).
+
+* Removed undocumented `--{tmm,tmi,tmd,tim,tii,tdm,tdd}` options from
+  hmmbuild.
+
+* Data serialization routines (used in `hmmpgmd`) were rewritten and
+  improved.
+
+
+For even more information, you can peruse the
+[git log for our develop branch](https://github.com/EddyRivasLab/hmmer/commits/develop).
+
+
--- a/Userguide.pdf
+++ b/Userguide.pdf
--- a/configure
+++ b/configure
--- a/configure.ac
+++ b/configure.ac
@@ -61,7 +61,6 @@ AC_PREREQ(2.63)
 # It's sort of standard to expect them in m4/, don't 
 # be confused that they're down in easel.
 #
-m4_include([easel/m4/ax_compiler_vendor.m4])
 m4_include([easel/m4/ax_gcc_func_attribute.m4])

 m4_include([easel/m4/esl_sse.m4])
@@ -70,12 +69,13 @@ m4_include([easel/m4/esl_vmx.m4])
 m4_include([easel/m4/ax_mpi.m4])
 m4_include([easel/m4/ax_pthread.m4])

+m4_include([easel/m4/esl_pic_flags.m4])

 ################################################################
 # 2. AC_INIT
 ################################################################

-AC_INIT(HMMER, 3.2.1, sean@eddylab.org, hmmer)
+AC_INIT(HMMER, 3.3, sean@eddylab.org, hmmer)
 AC_MSG_NOTICE([Configuring HMMER3 for your system.])

 # remember if the user is overriding CFLAGS
@@ -107,8 +107,8 @@ fi
 # to use HMMER as a library inside other packages, with no name clashes.
 ################################################################

-HMMER_DATE="June 2018"
-HMMER_COPYRIGHT="Copyright (C) 2018 Howard Hughes Medical Institute."
+HMMER_DATE="Nov 2019"
+HMMER_COPYRIGHT="Copyright (C) 2019 Howard Hughes Medical Institute."
 HMMER_LICENSE="Freely distributed under the BSD open source license."
 HMMER_VERSION=$PACKAGE_VERSION
 HMMER_URL="http://hmmer.org/"
@@ -116,10 +116,10 @@ HMMER_URL="http://hmmer.org/"
 HMMER_ESLDIR="easel"
 HMMER_SADIR="libdivsufsort"

-EASEL_DATE="June 2018"
-EASEL_COPYRIGHT="Copyright (C) 2018 Howard Hughes Medical Institute."
+EASEL_DATE="Nov 2019"
+EASEL_COPYRIGHT="Copyright (C) 2019 Howard Hughes Medical Institute."
 EASEL_LICENSE="Freely distributed under the BSD open source license."
-EASEL_VERSION="0.45h"
+EASEL_VERSION="0.46"
 EASEL_URL="http://bioeasel.org/"

 AC_SUBST(HMMER_DATE)
@@ -147,6 +147,7 @@ AC_DEFINE_UNQUOTED([EASEL_DATE],      ["$EASEL_DATE"],      [Easel release date]
 AC_DEFINE_UNQUOTED([EASEL_COPYRIGHT], ["$EASEL_COPYRIGHT"], [Easel copyright])
 AC_DEFINE_UNQUOTED([EASEL_LICENSE],   ["$EASEL_LICENSE"],   [Easel license])
 AC_DEFINE_UNQUOTED([EASEL_VERSION],   ["$EASEL_VERSION"],   [Easel version])
+AC_DEFINE_UNQUOTED([EASEL_URL],       ["$EASEL_URL"],       [Easel web URL])


 # Figure out what host we're compiling on.
@@ -199,10 +200,13 @@ AC_ARG_ENABLE(vmx,     [AS_HELP_STRING([--enable-vmx],     [enable our Altivec/V
 AC_ARG_ENABLE(threads, [AS_HELP_STRING([--enable-threads], [enable POSIX threads parallelization])],     enable_threads=$enableval, enable_threads=check)
 AC_ARG_ENABLE(mpi,     [AS_HELP_STRING([--enable-mpi],     [enable MPI parallelization])],               enable_mpi=$enableval,     enable_mpi=no)

+AC_ARG_ENABLE(pic,     [AS_HELP_STRING([--enable-pic],     [enable position-independent code])],         enable_pic=$enableval,     enable_pic=no)
+
 AC_ARG_WITH(gsl,       [AS_HELP_STRING([--with-gsl],       [use the GSL, GNU Scientific Library])],      with_gsl=$withval,         with_gsl=no)



+
 # If a vector implementation is force-selected, make sure only one is,
 # and turn off checking for the others.
 vecsel=0
@@ -221,19 +225,13 @@ fi
 ################################################################

 AC_PROG_CC
+AC_PROG_CC_STDC
 AC_PROG_CPP
 AC_PROG_INSTALL
 AC_PROG_RANLIB
 AC_PATH_PROG([AR], [ar], [:], [$PATH:/usr/ccs/bin:/usr/xpg4/bin])
 AC_PROG_LN_S

-# AC_PROG_CC_STDC wants to append -c99 to icc; icc doesn't like this.
-AX_COMPILER_VENDOR
-if test "$ax_cv_c_compiler_vendor" != "intel"; then
-  AC_PROG_CC_STDC
-fi
-
-
 # Select our default optimization flags in CFLAGS.
 #  --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
 #
@@ -276,6 +274,12 @@ if test "$enable_mpi" = "yes"; then
 fi


+# PIC (position-independent code) for shared library support
+#
+if test "$enable_pic" = "yes"; then
+   ESL_PIC_FLAGS
+fi
+

 # Support for POSIX multithreading (we should generally have this)
 #
@@ -409,6 +413,13 @@ else
  AC_DEFINE(HAVE_GZIP, 1, [Support external gzip decompression])
 fi

+# We need python 3 for 'make check' and some dev tools. sqc checks
+# too, as does the Makefile, but we also check in ./configure, so we
+# don't recommend 'make check' to the user if they can't use it.
+# 
+AC_CHECK_PROG(HAVE_PYTHON3, python3, yes)
+
+
 ################################################################
 # 6. Checks for libraries
 #################################################################
@@ -584,6 +595,7 @@ AC_CONFIG_FILES([ \
  documentation/Makefile                       \
  documentation/man/Makefile                   \
  documentation/userguide/Makefile             \
+  documentation/userguide/inclusions/Makefile  \
  libdivsufsort/Makefile                       \
  ])

@@ -599,6 +611,7 @@ AC_CONFIG_FILES([ \
 # HMMER_VERSION, HMMER_DATE, HMMER_COPYRIGHT
 AC_CONFIG_FILES([ \
  documentation/userguide/titlepage.tex  \
+  documentation/userguide/titlepage_daemon.tex  \
  documentation/userguide/copyright.tex  \
  ])

@@ -608,12 +621,14 @@ AC_CONFIG_FILES([ \
  documentation/man/alimask.man     \
  documentation/man/hmmalign.man    \
  documentation/man/hmmbuild.man    \
+  documentation/man/hmmc2.man       \
  documentation/man/hmmconvert.man  \
  documentation/man/hmmemit.man     \
  documentation/man/hmmer.man       \
  documentation/man/hmmfetch.man    \
  documentation/man/hmmlogo.man     \
  documentation/man/hmmpgmd.man     \
+  documentation/man/hmmpgmd_shard.man     \
  documentation/man/hmmpress.man    \
  documentation/man/hmmscan.man     \
  documentation/man/hmmsearch.man   \
@@ -642,6 +657,7 @@ AC_CONFIG_FILES([ \
  easel/miniapps/esl-construct.man   \
  easel/miniapps/esl-histplot.man    \
  easel/miniapps/esl-mask.man        \
+  easel/miniapps/esl-mixdchlet.man   \
  easel/miniapps/esl-reformat.man    \
  easel/miniapps/esl-selectn.man     \
  easel/miniapps/esl-seqrange.man    \
@@ -673,17 +689,25 @@ AC_OUTPUT
 echo "

 HMMER configuration:
-     compiler:             ${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} 
+   compiler:             ${CC} ${CFLAGS} ${SSE_CFLAGS} ${VMX_CFLAGS} ${PTHREAD_CFLAGS} ${PIC_CFLAGS}
   host:                 $host
   linker:               ${LDFLAGS}
   libraries:            ${LIBS} ${LIBGSL} ${PTHREAD_LIBS}
-     DP implementation:    ${impl_choice}
+   DP implementation:    ${impl_choice}"
+

-Do 'make'  to build HMMER, and optionally:
+if test x"$HAVE_PYTHON3" = x"yes"; then echo "
+Now do 'make'  to build HMMER, and optionally:
       'make check'  to run self tests,
       'make install'  to install programs and man pages,
       '(cd easel; make install)'  to install Easel tools.
-"
-
+";
+else echo "
+   (No python3 found, so 'make check' is disabled.)

+Now do 'make'  to build HMMER, and optionally:
+       'make install'  to install programs and man pages,
+       '(cd easel; make install)'  to install Easel tools.
+";
+fi

--- a/debian/changelog
+++ b/debian/changelog
+hmmer (3.3+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+
+  * New upstream version
+
+ -- Steffen Moeller <moeller@debian.org>  Fri, 22 Nov 2019 19:14:46 +0100
+
 hmmer (3.2.1+dfsg-3) unstable; urgency=medium

  [ Michael R. Crusoe ]

--- a/debian/copyright
+++ b/debian/copyright
@@ -4,6 +4,9 @@ Upstream-Contact: Sean R. Eddy <eddys@janelia.hhmi.org>
 Source: http://hmmer.org/download.html
 Files-Excluded: */libdivsufsort
                */.gitignore
+                configure
+                config.guess
+                config.sub

 Files: *
 Copyright: 1992-2010 Sean R. Eddy <eddy@genetics.wustl.edu>

--- a/debian/patches/hardening
+++ b/debian/patches/hardening
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Descriptions: Don't stomp on Debian's CFLAGS
+Index: hmmer/configure.ac
+===================================================================
 --- hmmer.orig/configure.ac
 +++ hmmer/configure.ac
-@@ -78,12 +78,6 @@
- AC_INIT(HMMER, 3.2.1, sean@eddylab.org, hmmer)
+@@ -78,12 +78,6 @@ m4_include([easel/m4/esl_pic_flags.m4])
+ AC_INIT(HMMER, 3.3, sean@eddylab.org, hmmer)
 AC_MSG_NOTICE([Configuring HMMER3 for your system.])
 
 -# remember if the user is overriding CFLAGS
@@ -15,7 +17,7 @@ Descriptions: Don't stomp on Debian's CFLAGS
 ################################################################
 # 3. Info on the package
 ################################################################
-@@ -236,21 +230,15 @@
+@@ -234,21 +228,15 @@ AC_PROG_LN_S
 #  --enable-gcov, --enable-gprof, and --enable-debugging are mutually exclusive.
 #
 if test "$enable_gcov" = "yes"; then

--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,5 +2,4 @@ fix_manpage_extension.patch
 use_debian_packaged_libdivsufsort.patch
 verbose-easel
 hardening
-spelling
 skip_threads_check
--- a/debian/patches/skip_threads_check
+++ b/debian/patches/skip_threads_check
@@ -2,9 +2,11 @@ Author: Michael R. Crusoe
 Last-Update: 2019-09-25 13:04:34 +0200
 Description: Skip check for threads

+Index: hmmer/testsuite/i19-hmmpgmd-ga.pl
+===================================================================
 --- hmmer.orig/testsuite/i19-hmmpgmd-ga.pl
 +++ hmmer/testsuite/i19-hmmpgmd-ga.pl
-@@ -53,11 +53,11 @@
+@@ -68,11 +68,11 @@ foreach $h3prog  (@h3progs) { if (! -x "
 # if not found, threads are not enabled and this
 # test would fail, but we return ok status 0 because
 # we don't want the full testsuite to fail.

--- a/debian/patches/spelling
+++ b/debian/patches/spelling
-From: Michael R. Crusoe <michael.crusoe@gmail.com>
-Subject: Debian Lintian inspired typo fixes
--- hmmer.orig/src/hmmdmstr.c
-+++ hmmer/src/hmmdmstr.c
-@@ -1252,7 +1252,7 @@
- 
-       /* skip leading white spaces */
-       while (*ptr == ' ' || *ptr == '\t') ++ptr;
-      if (!*ptr) { client_msg(fd, eslEINVAL, "Load command missing ip addres\n"); return; }
-+      if (!*ptr) { client_msg(fd, eslEINVAL, "Load command missing ip address\n"); return; }
- 
-       while (ptr && *ptr) {
- 	if (ip_addr != NULL) { client_msg(fd, eslEINVAL, "Multiple ip addresses on command line %s\n", s); return; }
--- hmmer.orig/src/nhmmer.c
-+++ hmmer/src/nhmmer.c
-@@ -358,7 +358,7 @@
- 
- #if defined (eslENABLE_SSE)
-   if (esl_opt_IsUsed(go, "--seed_max_depth")    && fprintf(ofp, "# FM Seed length:                  %d\n",             esl_opt_GetInteger(go, "--seed_max_depth"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
-  if (esl_opt_IsUsed(go, "--seed_sc_thresh")    && fprintf(ofp, "# FM score threshhold (bits):      %g\n",             esl_opt_GetReal(go, "--seed_sc_thresh"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
-+  if (esl_opt_IsUsed(go, "--seed_sc_thresh")    && fprintf(ofp, "# FM score threshold (bits):      %g\n",             esl_opt_GetReal(go, "--seed_sc_thresh"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
-   if (esl_opt_IsUsed(go, "--seed_sc_density")   && fprintf(ofp, "# FM score density (bits/pos):     %g\n",             esl_opt_GetReal(go, "--seed_sc_density"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
-   if (esl_opt_IsUsed(go, "--seed_drop_max_len") && fprintf(ofp, "# FM max neg-growth length:        %d\n",             esl_opt_GetInteger(go, "--seed_drop_max_len")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
-   if (esl_opt_IsUsed(go, "--seed_drop_lim")     && fprintf(ofp, "# FM max run drop:                 %g\n",             esl_opt_GetReal(go, "--seed_drop_lim"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
--- a/debian/patches/use_debian_packaged_libdivsufsort.patch
+++ b/debian/patches/use_debian_packaged_libdivsufsort.patch
@@ -2,17 +2,19 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Sun, 26 Jun 2016 00:53:18 +0200
 Description: Use Debian packaged libdivsufsort

+Index: hmmer/configure.ac
+===================================================================
 --- hmmer.orig/configure.ac
 +++ hmmer/configure.ac
-@@ -114,7 +114,6 @@
+@@ -114,7 +114,6 @@ HMMER_VERSION=$PACKAGE_VERSION
 HMMER_URL="http://hmmer.org/"
 
 HMMER_ESLDIR="easel"
 -HMMER_SADIR="libdivsufsort"
 
- EASEL_DATE="June 2018"
- EASEL_COPYRIGHT="Copyright (C) 2018 Howard Hughes Medical Institute."
-@@ -129,7 +128,6 @@
+ EASEL_DATE="Nov 2019"
+ EASEL_COPYRIGHT="Copyright (C) 2019 Howard Hughes Medical Institute."
+@@ -129,7 +128,6 @@ AC_SUBST(HMMER_VERSION)
 AC_SUBST(HMMER_URL)
 
 AC_SUBST(HMMER_ESLDIR)
@@ -20,15 +22,15 @@ Description: Use Debian packaged libdivsufsort
 
 AC_SUBST(EASEL_DATE)
 AC_SUBST(EASEL_COPYRIGHT)
-@@ -584,7 +582,6 @@
-   documentation/Makefile            \
+@@ -596,7 +594,6 @@ AC_CONFIG_FILES([ \
   documentation/man/Makefile                   \
   documentation/userguide/Makefile             \
+   documentation/userguide/inclusions/Makefile  \
 -  libdivsufsort/Makefile                       \
   ])
 
 # Easel Makefiles.
-@@ -656,7 +653,6 @@
+@@ -672,7 +669,6 @@ AC_CONFIG_FILES([ \
 AC_CONFIG_HEADERS([easel/decoy_config.h])   # Put this first to keep gnu 'autoheader' from overwriting a real config file.
 AC_CONFIG_HEADERS([src/p7_config.h])
 AC_CONFIG_HEADERS([easel/esl_config.h])
@@ -36,9 +38,11 @@ Description: Use Debian packaged libdivsufsort
 
 # the following incantation establishes a symlink of
 # src/impl_{whatever} to src/impl in the *build* directory.
+Index: hmmer/Makefile.in
+===================================================================
 --- hmmer.orig/Makefile.in
 +++ hmmer/Makefile.in
-@@ -26,8 +26,6 @@
+@@ -26,8 +26,6 @@ SHELL          = /bin/sh
 # location of easel
 ESLDIR         = @HMMER_ESLDIR@
 
@@ -47,7 +51,7 @@ Description: Use Debian packaged libdivsufsort
 
 
 # Package information
-@@ -88,7 +86,6 @@
+@@ -88,7 +86,6 @@ endif
 #
 all: 
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} all
@@ -55,7 +59,7 @@ Description: Use Debian packaged libdivsufsort
 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} all
 
-@@ -96,7 +93,6 @@
+@@ -96,7 +93,6 @@ all:
 #
 dev: 
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} dev
@@ -63,15 +67,15 @@ Description: Use Debian packaged libdivsufsort
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} dev
 	${QUIET_SUBDIR0}profmark   ${QUIET_SUBDIR1} dev
 
-@@ -110,7 +106,6 @@
- #
+@@ -111,7 +107,6 @@ tests:
 check:
+ 	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
 -	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all	
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} check
 	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} check
-@@ -148,7 +143,6 @@
+@@ -149,7 +144,6 @@ clean:
 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} clean
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} clean
@@ -79,7 +83,7 @@ Description: Use Debian packaged libdivsufsort
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
 ifndef V
 	@echo '     ' CLEAN hmmer
-@@ -162,7 +156,6 @@
+@@ -163,7 +157,6 @@ distclean:
 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} distclean
@@ -87,9 +91,11 @@ Description: Use Debian packaged libdivsufsort
 	${QUIET}-rm config.log config.status
 	${QUIET}-rm -rf autom4te.cache
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
+Index: hmmer/src/Makefile.in
+===================================================================
 --- hmmer.orig/src/Makefile.in
 +++ hmmer/src/Makefile.in
-@@ -36,11 +36,9 @@
+@@ -37,11 +37,9 @@ INSTALL   = @INSTALL@
 
 IMPLDIR   = impl_@IMPL_CHOICE@
 ESLDIR    = @HMMER_ESLDIR@

--- a/debian/patches/verbose-easel
+++ b/debian/patches/verbose-easel
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
+Index: hmmer/Makefile.in
+===================================================================
 --- hmmer.orig/Makefile.in
 +++ hmmer/Makefile.in
-@@ -67,16 +67,16 @@
+@@ -67,16 +67,16 @@ INSTALL   = @INSTALL@
 
 # beautification magic stolen from git 
 #
@@ -22,7 +24,7 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 endif
 
 .PHONY: all dev check pdf install uninstall clean distclean TAGS
-@@ -85,35 +85,35 @@
+@@ -85,36 +85,36 @@ endif
 #      (Excludes test programs.)
 #
 all: 
@@ -54,6 +56,7 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 # check: Run test suites.
 #
 check:
+ 	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 -	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
 -	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
 -	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} check
@@ -71,8 +74,8 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 
 # install: binaries in ${bindir}/, man pages in ${man1dir}/
 #          Creates these directories if they don't exist.
-@@ -126,8 +126,8 @@
- install: 
+@@ -127,8 +127,8 @@ pdf:
+ install: all
 	${INSTALL} -d ${DESTDIR}${bindir}
 	${INSTALL} -d ${DESTDIR}${man1dir}
 -	${MAKE} -C src install
@@ -82,7 +85,7 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 
 # uninstall: reverses the steps of "make install".
 #
-@@ -138,11 +138,11 @@
+@@ -139,11 +139,11 @@ uninstall:
 # "make clean" removes almost everything except configuration files.
 #
 clean:
@@ -99,9 +102,11 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
 ifndef V
 	@echo '     ' CLEAN hmmer
+Index: hmmer/easel/Makefile.in
+===================================================================
 --- hmmer.orig/easel/Makefile.in
 +++ hmmer/easel/Makefile.in
-@@ -80,7 +80,7 @@
+@@ -80,7 +80,7 @@ INSTALL  = @INSTALL@
 
 # beautification magic, stolen from git
 #
@@ -110,7 +115,7 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 QUIET_SUBDIR1 =
 ifndef V
 	QUIET         = @
-@@ -89,7 +89,7 @@
+@@ -89,7 +89,7 @@ ifndef V
 	QUIET_AR      = @echo '    ' AR $@;
 	QUIET_SUBDIR0 = +@subdir=
 	QUIET_SUBDIR1 = ; echo '    ' SUBDIR  $$subdir; \
@@ -119,38 +124,7 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 endif
 
 
-@@ -495,24 +495,24 @@
- .FORCE:
- 
- all:    libeasel.a .FORCE
-	${QUIET_SUBDIR0}miniapps  ${QUIET_SUBDIR1} all
-+	+${QUIET_SUBDIR0}miniapps  ${QUIET_SUBDIR1} all
- 
- dev:    libeasel.a ${ALL_UTESTS} ${BENCHMARKS} ${EXPERIMENTS} ${EXAMPLES} .FORCE
-	${QUIET_SUBDIR0}miniapps  ${QUIET_SUBDIR1} dev
-+	+${QUIET_SUBDIR0}miniapps  ${QUIET_SUBDIR1} dev
- 
- tests:  ${ALL_UTESTS} 
-	${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} tests
-+	+${QUIET_SUBDIR0}miniapps ${QUIET_SUBDIR1} tests
- 
- check:  ${ALL_UTESTS} .FORCE
-	${QUIET_SUBDIR0}miniapps  ${QUIET_SUBDIR1} check
-	${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
-+	+${QUIET_SUBDIR0}miniapps  ${QUIET_SUBDIR1} check
-+	+${QUIET_SUBDIR0}testsuite ${QUIET_SUBDIR1} check
- 
- # `make dcheck`: run developer testsuite, save output in testsuite/dcheck.report
- dcheck:
- 	${QUIET_SUBDIR0}testsuite   ${QUIET_SUBDIR1} dcheck
- 
- pdf:
-	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
-+	+${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
- 
- libeasel.a:  ${ALL_OBJS} 
- 	${QUIET_AR}${AR} -r libeasel.a $(ALL_OBJS) > /dev/null 2>&1
-@@ -599,7 +599,7 @@
+@@ -629,7 +629,7 @@ ${ALL_EXAMPLES}: libeasel.a
 install:
 	${INSTALL} -d ${DESTDIR}${bindir}
 	${INSTALL} -d ${DESTDIR}${man1dir}
@@ -159,9 +133,11 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 
 uninstall:
 	${MAKE} -C miniapps uninstall
+Index: hmmer/src/Makefile.in
+===================================================================
 --- hmmer.orig/src/Makefile.in
 +++ hmmer/src/Makefile.in
-@@ -217,7 +217,7 @@
+@@ -230,7 +230,7 @@ EXAMPLES = \
 	p7_spensemble_example
 
 # beautification magic stolen from git
@@ -170,7 +146,7 @@ Subject: Allow the easel Makefile to be verbosely run from the hmmer Makefile
 QUIET_SUBDIR1 = 
 ifndef V
 	QUIET_CC      = @echo '    ' CC $@;
-@@ -225,7 +225,7 @@
+@@ -238,7 +238,7 @@ ifndef V
 	QUIET_AR      = @echo '    ' AR $@;
 	QUIET_SUBDIR0 = +@subdir=
 	QUIET_SUBDIR1 = ; echo '    ' SUBDIR $$subdir; \

--- a/debian/rules
+++ b/debian/rules
@@ -49,7 +49,7 @@ override_dh_auto_clean:
 	rm -f testsuite/esltmp*
 	rm -f easel/testsuite/esltmp*
 	rm -f tutorial/MADE1.hmm.h3?
-	rm -f config.log config.status
+	rm -f config.log config.status configure config.guess config.sub
 	find . -name Makefile -delete

 override_dh_compress:

--- a/documentation/man/Makefile.in
+++ b/documentation/man/Makefile.in
@@ -23,11 +23,13 @@ INSTALL     = @INSTALL@
 MANS =  hmmer\
 	hmmalign\
 	hmmbuild\
+	hmmc2\
 	hmmconvert\
 	hmmemit\
 	hmmfetch\
 	hmmlogo\
 	hmmpgmd\
+	hmmpgmd_shard\
 	hmmpress\
 	hmmscan\
 	hmmsearch\