Updates versioning to 3.2.1, including user guide and its inclusions.

EddyRivasLab · Jun 11, 2018 · f2f1957 · f2f1957
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diff --git a/INSTALL b/INSTALL
@@ -1,10 +1,10 @@
 Brief installation instructions 
-HMMER 3.2 (June 2018)
+HMMER 3.2.1 (June 2018)
 
-Starting from a source distribution, hmmer-3.2.tar.gz:
-   uncompress hmmer-3.2.tar.gz  
-   tar xf hmmer-3.2.tar
-   cd hmmer-3.2
+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
    ./configure
    make
    make check                        # optional: automated tests

diff --git a/README.md b/README.md
@@ -16,13 +16,12 @@ depends on the Easel library, also at
 [github](https://github.com/EddyRivasLab/easel).
 
 
-
 ### to download and build the current source code release:
 
-```bash
+```
    % wget http://eddylab.org/software/hmmer/hmmer.tar.gz
    % tar zxf hmmer.tar.gz
-   % cd hmmer-3.2
+   % cd hmmer-3.2.1
    % ./configure --prefix /your/install/path
    % make
    % make check                 # optional: run automated tests
@@ -34,7 +33,7 @@ Executable programs will be installed in `/your/install/path/bin`. If
 you leave this optional `./configure` argument off, the default prefix
 is `/usr/local`.
 
-Files to read in the top-level source directory:
+Files to read in the source directory:
 
    * INSTALL - brief installation instructions.
    * Userguide.pdf - the HMMER User's Guide.
@@ -46,9 +45,12 @@ HMMER User's Guide (Userguide.pdf).
 
 ### to clone a copy of HMMER3 source from github:
 
-You need to clone both the HMMER and Easel repositories, as follows:
+The tarball way, above, is a better way to install HMMER (it includes
+a precompiled Userguide.pdf, for example), but you can also clone our
+github repo. You need to clone both the HMMER and Easel repositories,
+as follows:
 
-```bash
+```
    % git clone https://github.com/EddyRivasLab/hmmer
    % cd hmmer
    % git clone https://github.com/EddyRivasLab/easel

diff --git a/configure.ac b/configure.ac
@@ -75,7 +75,7 @@ m4_include([easel/m4/ax_pthread.m4])
 # 2. AC_INIT
 ################################################################
 
-AC_INIT(HMMER, 3.2.1-dev, sean@eddylab.org, hmmer)
+AC_INIT(HMMER, 3.2.1, sean@eddylab.org, hmmer)
 AC_MSG_NOTICE([Configuring HMMER3 for your system.])
 
 # remember if the user is overriding CFLAGS
@@ -119,7 +119,7 @@ HMMER_SADIR="libdivsufsort"
 EASEL_DATE="June 2018"
 EASEL_COPYRIGHT="Copyright (C) 2018 Howard Hughes Medical Institute."
 EASEL_LICENSE="Freely distributed under the BSD open source license."
-EASEL_VERSION="0.45-dev"
+EASEL_VERSION="0.45h"
 EASEL_URL="http://bioeasel.org/"
 
 AC_SUBST(HMMER_DATE)

diff --git a/documentation/userguide/inclusions/hmmbuild-globins.out b/documentation/userguide/inclusions/hmmbuild-globins.out
@@ -1,5 +1,5 @@
 # hmmbuild :: profile HMM construction from multiple sequence alignments
-# HMMER 3.2 (June 2018); http://hmmer.org/
+# HMMER 3.2.1 (June 2018); http://hmmer.org/
 # Copyright (C) 2018 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/documentation/userguide/inclusions/hmmbuild-globins.out2 b/documentation/userguide/inclusions/hmmbuild-globins.out2
@@ -1,4 +1,4 @@
-HMMER3/f [3.2 | June 2018]
+HMMER3/f [3.2.1 | June 2018]
 NAME  globins4
 LENG  149
 ALPH  amino
@@ -7,7 +7,7 @@ MM    no
 CONS  yes
 CS    no
 MAP   yes
-DATE  Tue May 29 20:41:39 2018
+DATE  Mon Jun 11 19:15:50 2018
 NSEQ  4
 EFFN  0.964844
 CKSUM 2027839109

diff --git a/documentation/userguide/inclusions/hmmbuild-made1.out b/documentation/userguide/inclusions/hmmbuild-made1.out
@@ -1,5 +1,5 @@
 # hmmbuild :: profile HMM construction from multiple sequence alignments
-# HMMER 3.2 (June 2018); http://hmmer.org/
+# HMMER 3.2.1 (June 2018); http://hmmer.org/
 # Copyright (C) 2018 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -9,6 +9,6 @@
 
 # idx name                  nseq  alen  mlen     W eff_nseq re/pos description
 #---- -------------------- ----- ----- ----- ----- -------- ------ -----------
-1     MADE1                  100   304    80   473     3.55  0.709 MADE1 (MAriner Derived Element 1), a TcMar-Mariner ...
+1     MADE1                  100   304    80   474     3.58  0.708 MADE1 (MAriner Derived Element 1), a TcMar-Mariner ...
 
-# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
+# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
diff --git a/documentation/userguide/inclusions/hmmscan-minifam-sevenless.out b/documentation/userguide/inclusions/hmmscan-minifam-sevenless.out
@@ -1,5 +1,5 @@
 # hmmscan :: search sequence(s) against a profile database
-# HMMER 3.2 (June 2018); http://hmmer.org/
+# HMMER 3.2.1 (June 2018); http://hmmer.org/
 # Copyright (C) 2018 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/documentation/userguide/inclusions/hmmscan-noargs.out b/documentation/userguide/inclusions/hmmscan-noargs.out
@@ -1,5 +1,5 @@
 # hmmscan :: search sequence(s) against a profile database
-# HMMER 3.2 (June 2018); http://hmmer.org/
+# HMMER 3.2.1 (June 2018); http://hmmer.org/
 # Copyright (C) 2018 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/documentation/userguide/inclusions/hmmsearch-globins.out b/documentation/userguide/inclusions/hmmsearch-globins.out
@@ -1,5 +1,5 @@
 # hmmsearch :: search profile(s) against a sequence database
-# HMMER 3.2 (June 2018); http://hmmer.org/
+# HMMER 3.2.1 (June 2018); http://hmmer.org/
 # Copyright (C) 2018 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/documentation/userguide/inclusions/hmmsearch-globins.out3 b/documentation/userguide/inclusions/hmmsearch-globins.out3
@@ -8,7 +8,7 @@ Passed Vit filter:                      2368  (0.00425268); expected 556.8 (0.00
 Passed Fwd filter:                      1127  (0.00202398); expected 5.6 (1e-05)
 Initial search space (Z):             556825  [actual number of targets]
 Domain search space  (domZ):            1126  [number of targets reported over threshold]
-# CPU time: 2.57u 0.09s 00:00:02.65 Elapsed: 00:00:01.10
-# Mc/sec: 26954.42
+# CPU time: 2.63u 0.07s 00:00:02.70 Elapsed: 00:00:01.10
+# Mc/sec: 26954.48
 //
 [ok]
diff --git a/documentation/userguide/inclusions/inclusions.def b/documentation/userguide/inclusions/inclusions.def
@@ -1,7 +1,7 @@
 \newcommand{\UNIrelease}{2018\_02}
 \newcommand{\UNInseq}{556,825}
 
-\newcommand{\HMMERversion}{3.2}
+\newcommand{\HMMERversion}{3.2.1}
 \newcommand{\HMMERdate}{June 2018}
 
 \newcommand{\BGLnseq}{4}
@@ -12,7 +12,7 @@
 \newcommand{\BGLre}{0.589}
 
 \newcommand{\HMMERfmtversion}{f}
-\newcommand{\HMMERsavestamp}{[3.2 | June 2018]}
+\newcommand{\HMMERsavestamp}{[3.2.1 | June 2018]}
 
 \newcommand{\SGUevalue}{6.7e-65}
 \newcommand{\SGUbitscore}{222.7}
@@ -62,10 +62,10 @@
 \newcommand{\NMHbto}{302389}
 \newcommand{\NMHnres}{660000}
 \newcommand{\NMHntop}{330000}
-\newcommand{\NMHnssv}{69202}
-\newcommand{\NMHfracssv}{10.5}
-\newcommand{\NMHnbias}{57239}
-\newcommand{\NMHfracbias}{8.7}
-\newcommand{\NMHnvit}{5181}
-\newcommand{\NMHfracvit}{0.8}
-\newcommand{\NMHnfwd}{3187}
+\newcommand{\NMHnssv}{76413}
+\newcommand{\NMHfracssv}{11.6}
+\newcommand{\NMHnbias}{56984}
+\newcommand{\NMHfracbias}{8.6}
+\newcommand{\NMHnvit}{5675}
+\newcommand{\NMHfracvit}{0.9}
+\newcommand{\NMHnfwd}{3194}
diff --git a/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out b/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out
@@ -1,5 +1,5 @@
 # jackhmmer :: iteratively search a protein sequence against a protein database
-# HMMER 3.2 (June 2018); http://hmmer.org/
+# HMMER 3.2.1 (June 2018); http://hmmer.org/
 # Copyright (C) 2018 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out4 b/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out4
@@ -2,8 +2,8 @@ Scores for complete sequences (score includes all domains):
    --- full sequence ---   --- best 1 domain ---    -#dom-
     E-value  score  bias    E-value  score  bias    exp  N  Sequence              Description
     ------- ------ -----    ------- ------ -----   ---- --  --------              -----------
-    4.7e-68  232.8   0.2    5.3e-68  232.6   0.2    1.0  1  sp|P02055|HBB_MELME    Hemoglobin subunit beta OS=Meles meles
-    7.1e-68  232.2   0.4    7.9e-68  232.1   0.4    1.0  1  sp|P81042|HBE_MACEU    Hemoglobin subunit epsilon OS=Macropus
-      9e-68  231.9   0.3      1e-67  231.7   0.3    1.0  1  sp|P15449|HBB_MELCA    Hemoglobin subunit beta OS=Mellivora c
-    1.3e-67  231.4   0.2    1.4e-67  231.3   0.2    1.0  1  sp|P68046|HBB_ODORO    Hemoglobin subunit beta OS=Odobenus ro
+    4.8e-68  232.8   0.2    5.4e-68  232.6   0.2    1.0  1  sp|P02055|HBB_MELME    Hemoglobin subunit beta OS=Meles meles
+    7.2e-68  232.2   0.4      8e-68  232.0   0.4    1.0  1  sp|P81042|HBE_MACEU    Hemoglobin subunit epsilon OS=Macropus
+    9.2e-68  231.9   0.3      1e-67  231.7   0.3    1.0  1  sp|P15449|HBB_MELCA    Hemoglobin subunit beta OS=Mellivora c
+    1.3e-67  231.4   0.2    1.4e-67  231.2   0.2    1.0  1  sp|P68046|HBB_ODORO    Hemoglobin subunit beta OS=Odobenus ro
 ...
diff --git a/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out5 b/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out5
@@ -1,15 +1,15 @@
 ...
-    3.2e-30  110.1   0.0    3.5e-30  110.0   0.0    1.0  1  sp|Q9DEP1|MYG_PSEGE    Myoglobin OS=Pseudochaenichthys georgi
+    3.1e-30  110.1   0.0    3.4e-30  110.0   0.0    1.0  1  sp|Q9DEP1|MYG_PSEGE    Myoglobin OS=Pseudochaenichthys georgi
     4.2e-30  109.7   0.3    5.7e-30  109.3   0.3    1.2  1  sp|P21199|GLB3_MORMR   Globin-3 OS=Mordacia mordax OX=7755 PE
-+   9.9e-30  108.5   0.2    1.1e-29  108.3   0.2    1.0  1  sp|P14397|MYG_GALGA    Myoglobin OS=Galeorhinus galeus OX=860
-    1.1e-29  108.4   0.0    1.2e-29  108.2   0.0    1.0  1  sp|Q9DEP0|MYG_CRYAN    Myoglobin OS=Cryodraco antarcticus OX=
-    1.6e-29  107.8   0.0    1.8e-29  107.7   0.0    1.0  1  sp|P02022|HBAM_LITCT   Hemoglobin heart muscle subunit alpha-
-+   3.4e-29  106.8   0.1    3.8e-29  106.6   0.1    1.0  1  sp|P14398|MYG_HEMJP    Myoglobin OS=Hemitriakis japanica OX=3
-    1.6e-28  104.6   0.0    1.9e-28  104.4   0.0    1.0  1  sp|P09106|HBAT_PAPAN   Hemoglobin subunit theta-1 OS=Papio an
-    3.2e-28  103.6   0.0    3.9e-28  103.3   0.0    1.0  1  sp|P0C227|GLB_NERAL    Globin OS=Nerita albicilla OX=52928 PE
-    3.9e-28  103.3   0.3    5.2e-28  102.9   0.3    1.0  1  sp|P80017|GLBD_MOLAR   Globin D, coelomic OS=Molpadia arenico
-    5.9e-26   96.2   0.6      1e-25   95.5   0.6    1.4  1  sp|C0HJZ2|HBA_SOMMI    Hemoglobin subunit alpha (Fragments) O
-    2.8e-25   94.1   0.2      3e-25   93.9   0.2    1.0  1  sp|P18979|HBA1_SAAHA   Hemoglobin subunit alpha-1 (Fragment) 
++   9.8e-30  108.5   0.2    1.1e-29  108.4   0.2    1.0  1  sp|P14397|MYG_GALGA    Myoglobin OS=Galeorhinus galeus OX=860
+    1.1e-29  108.4   0.0    1.2e-29  108.3   0.0    1.0  1  sp|Q9DEP0|MYG_CRYAN    Myoglobin OS=Cryodraco antarcticus OX=
+    1.6e-29  107.8   0.0    1.8e-29  107.6   0.0    1.0  1  sp|P02022|HBAM_LITCT   Hemoglobin heart muscle subunit alpha-
++   3.4e-29  106.8   0.1    3.7e-29  106.6   0.1    1.0  1  sp|P14398|MYG_HEMJP    Myoglobin OS=Hemitriakis japanica OX=3
+    1.6e-28  104.6   0.0    1.9e-28  104.3   0.0    1.0  1  sp|P09106|HBAT_PAPAN   Hemoglobin subunit theta-1 OS=Papio an
+    3.4e-28  103.5   0.0    4.2e-28  103.2   0.0    1.0  1  sp|P0C227|GLB_NERAL    Globin OS=Nerita albicilla OX=52928 PE
+    3.8e-28  103.3   0.3    5.1e-28  102.9   0.3    1.0  1  sp|P80017|GLBD_MOLAR   Globin D, coelomic OS=Molpadia arenico
+      6e-26   96.2   0.6      1e-25   95.4   0.6    1.4  1  sp|C0HJZ2|HBA_SOMMI    Hemoglobin subunit alpha (Fragments) O
+    2.9e-25   94.0   0.2    3.1e-25   93.9   0.2    1.0  1  sp|P18979|HBA1_SAAHA   Hemoglobin subunit alpha-1 (Fragment) 
 +   3.6e-24   90.4   0.0    4.3e-24   90.2   0.0    1.0  1  sp|Q90W04|NGB_TETNG    Neuroglobin OS=Tetraodon nigroviridis 
-    6.9e-24   89.5   0.0    8.2e-24   89.3   0.0    1.0  1  sp|P59742|NGB1_ONCMY   Neuroglobin-1 OS=Oncorhynchus mykiss O
+    6.8e-24   89.5   0.0    8.2e-24   89.3   0.0    1.0  1  sp|P59742|NGB1_ONCMY   Neuroglobin-1 OS=Oncorhynchus mykiss O
 ...
diff --git a/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out6 b/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out6
@@ -1,9 +1,9 @@
 @@ New targets included:   172
-@@ New alignment includes: 1126 subseqs (was 954), including original query
+@@ New alignment includes: 1129 subseqs (was 954), including original query
 @@ Continuing to next round.
 
 @@
 @@ Round:                  3
-@@ Included in MSA:        1126 subsequences (query + 1125 subseqs from 1125 targets)
+@@ Included in MSA:        1129 subsequences (query + 1128 subseqs from 1125 targets)
 @@ Model size:             146 positions
 @@
diff --git a/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out7 b/documentation/userguide/inclusions/jackhmmer-hbb-uniprot.out7
@@ -1,4 +1,4 @@
-@@ New targets included:   2
-@@ New alignment includes: 1168 subseqs (was 1167), including original query
+@@ New targets included:   1
+@@ New alignment includes: 1172 subseqs (was 1171), including original query
 //
 [ok]
diff --git a/documentation/userguide/inclusions/nhmmer-made1.out b/documentation/userguide/inclusions/nhmmer-made1.out
@@ -1,8 +1,8 @@
     E-value  score  bias  Sequence        start    end  Description
     ------- ------ -----  --------        -----  -----  -----------
     1.3e-10   38.3   7.0  humanchr1_frag 302390 302466 
-    6.4e-08   29.7   8.2  humanchr1_frag 174456 174498 
-    8.6e-08   29.3   6.2  humanchr1_frag 302466 302389 
-    3.8e-06   24.0   7.0  humanchr1_frag 174493 174456 
+    5.9e-08   29.8   8.2  humanchr1_frag 174456 174498 
+    8.2e-08   29.3   6.2  humanchr1_frag 302466 302389 
+    3.9e-06   23.9   7.0  humanchr1_frag 174493 174456 
   ------ inclusion threshold ------
-       0.69    7.1   7.8  humanchr1_frag 304073 304103 
+       0.67    7.2   7.8  humanchr1_frag 304073 304103 
diff --git a/documentation/userguide/inclusions/nhmmer-made1.out4 b/documentation/userguide/inclusions/nhmmer-made1.out4
@@ -4,4 +4,4 @@
            MADE1      4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80    
                         ggt ggtgcaaaa  aattg ggtttttgccatt cttttaat gc    aaaa      a t ctttt caccaa ctaa
   humanchr1_frag 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttAAAAG----TAATGCTTTTACACCAATCTAA 302466
-                        89*******************************************9777666663....355789*************996 PP
+                        89*******************************************9777666663....355789*************986 PP
diff --git a/documentation/userguide/inclusions/nhmmer-made1.out5 b/documentation/userguide/inclusions/nhmmer-made1.out5
@@ -2,12 +2,12 @@ Internal pipeline statistics summary:
 -------------------------------------
 Query model(s):                            1  (80 nodes)
 Target sequences:                          1  (660000 residues searched)
-Residues passing SSV filter:           69202  (0.105); expected (0.02)
-Residues passing bias filter:          57239  (0.0867); expected (0.02)
-Residues passing Vit filter:            5181  (0.00785); expected (0.003)
-Residues passing Fwd filter:            3187  (0.00483); expected (3e-05)
+Residues passing SSV filter:           76413  (0.116); expected (0.02)
+Residues passing bias filter:          56984  (0.0863); expected (0.02)
+Residues passing Vit filter:            5675  (0.0086); expected (0.003)
+Residues passing Fwd filter:            3194  (0.00484); expected (3e-05)
 Total number of hits:                      6  (0.000498)
-# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.01
-# Mc/sec: 3017.39
+# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
+# Mc/sec: 3878.38
 //
 [ok]
diff --git a/documentation/userguide/install.tex b/documentation/userguide/install.tex
@@ -36,14 +36,14 @@ \section{Quick-ish: compile the source code}
 You can obtain the source code as a compressed \mono{.tar.gz} tarball
 from \href{http://hmmer.org}{hmmer.org} in your browser, or you can also
 \mono{wget} it on the command line from
-\href{http://eddylab.org/software/hmmer/hmmer-3.2.tar.gz}{eddylab.org/software/hmmer/hmmer-3.2.tar.gz}.
-Uncompress and untar it, and switch into the \mono{hmmer-3.2}
+\href{http://eddylab.org/software/hmmer/hmmer-\HMMERversion{}.tar.gz}{eddylab.org/software/hmmer/hmmer-\HMMERversion{}.tar.gz}.
+Uncompress and untar it, and switch into the \mono{hmmer-\HMMERversion{}}
 directory.  For example:
 
   \vspace{1ex}
-  \user{\% wget http://eddylab.org/software/hmmer/hmmer-3.2.tar.gz}\\
-  \user{\% tar xf hmmer-3.2.tar.gz}\\
-  \user{\% cd hmmer-3.2}
+  \user{\% wget http://eddylab.org/software/hmmer/hmmer-\HMMERversion{}.tar.gz}\\
+  \user{\% tar xf hmmer-\HMMERversion{}.tar.gz}\\
+  \user{\% cd hmmer-\HMMERversion{}}
   \vspace{1ex}
 
 To compile:
@@ -104,8 +104,8 @@ \section{Geeky: compile source from our github repository}
   in the past.}
 
   \vspace{1ex}
-  \user{\% git clone https://github.com/EddyRivasLab/hmmer hmmer-3.2} \\
-  \user{\% cd hmmer-3.2}
+  \user{\% git clone https://github.com/EddyRivasLab/hmmer hmmer-\HMMERversion{}} \\
+  \user{\% cd hmmer-\HMMERversion{}}
   \vspace{1ex}
 
 This is now essentially the same as if you unpacked a tarball, so from
@@ -382,14 +382,14 @@ \subsection{What gets installed by \mono{make install}, and where?}
 like:
 
   \vspace{1ex}
-  \user{\% ./configure {-}{-}prefix /usr/local/hmmer-3.2}
+  \user{\% ./configure {-}{-}prefix /usr/local/hmmer-\HMMERversion{}}
   \vspace{1ex}
 
 That would keep HMMER out of your system-wide directories, which might
 be desirable. This is a simple way to install multiple versions of
 HMMER, for example, without having them clobber each other.  Then
-you'd add \mono{/usr/local/hmmer-3.2/bin} to your \mono{PATH} and
-\mono{/usr/local/hmmer-3.2/share/man} to your \mono{MANPATH}.
+you'd add \mono{/usr/local/hmmer-\HMMERversion{}/bin} to your \mono{PATH} and
+\mono{/usr/local/hmmer-\HMMERversion{}/share/man} to your \mono{MANPATH}.
 
 Again, these variables only affect where \mono{make install} copies
 stuff. HMMER and Easel programs have no pathnames compiled into them.
@@ -419,7 +419,7 @@ \subsection{Installing both HMMER2 and HMMER3}
 and \mono{hmmsearch}.
 
 One workaround is to install the two packages each in their own
-hierarchy, as above: \mono{./configure --prefix=somewhere/hmmer-3.2}
+hierarchy, as above: \mono{./configure --prefix=somewhere/hmmer-\HMMERversion{}}
 for HMMER3, and \mono{./configure --prefix=somewhere/hmmer-2.3.2} for
 HMMER2. One set of programs could be in your \mono{PATH}, and you
 could call the others using full pathnames.

diff --git a/release-notes/RELEASE-3.2.1 b/release-notes/RELEASE-3.2.1
@@ -1,18 +1,12 @@
 HMMER 3.2.1 release notes    (Jun 2018)
-Update release for HMMER 3.2 (Jun 2018)
-Previous release was 3.1b2   (Mar 2015)
 http://hmmer.org
 
-
-
-Release 3.2.1:
---------------
-
-* Removes --fast and --symfrac options from jackhmmer and its
-  documentation. Fixes issue #140, jackhmmer --fast segfault.
-
-* Fixes compilation failures on i586, ppc64be. (issues #141, #120)
-
+Release 3.2.1 fixes:
+----------------------
+* 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.