Index: head/biology/hmmer/files/patch-configure
===================================================================
--- head/biology/hmmer/files/patch-configure	(revision 474454)
+++ head/biology/hmmer/files/patch-configure	(nonexistent)
@@ -1,10 +0,0 @@
---- configure.orig	2015-02-26 12:45:55 UTC
-+++ configure
-@@ -3912,6 +3912,7 @@ fi
- if test "$impl_choice" = "none"; then
-   case $host in
-     ia64-*-*)      impl_choice=sse;;
-+    amd64-*-*)     impl_choice=sse;;
-     i?86-*-*)      impl_choice=sse;;
-     x86*-*-*)      impl_choice=sse;;
-     powerpc*-*-*)  impl_choice=vmx;;

Property changes on: head/biology/hmmer/files/patch-configure
___________________________________________________________________
Deleted: fbsd:nokeywords
## -1 +0,0 ##
-yes
\ No newline at end of property
Deleted: svn:eol-style
## -1 +0,0 ##
-native
\ No newline at end of property
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: head/biology/hmmer/Makefile
===================================================================
--- head/biology/hmmer/Makefile	(revision 474454)
+++ head/biology/hmmer/Makefile	(revision 474455)
@@ -1,43 +1,50 @@
 # Created by: barnhart@genetics.wustl.edu
 # $FreeBSD$
 
 PORTNAME=	hmmer
-PORTVERSION=	3.1b2
+PORTVERSION=	3.2.1
 CATEGORIES=	biology
-MASTER_SITES=	http://eddylab.org/software/hmmer3/${PORTVERSION}/
+MASTER_SITES=	http://eddylab.org/software/hmmer/
 
 MAINTAINER=	mzaki@niid.go.jp
 COMMENT=	Profile hidden Markov models for biological sequence analysis
 
-LICENSE=	GPLv3
+LICENSE=	BSD3CLAUSE
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-USES=		gmake
+ONLY_FOR_ARCHS=	amd64 i386 ia64 powerpc powerpc64
+ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions
+
+USES=		gmake perl5 shebangfix
+
 GNU_CONFIGURE=	yes
 MAKE_ARGS=	V=1
 
+TEST_TARGET=	check
+USE_PERL5=	test
+SHEBANG_GLOB=	*.pl
+SHEBANG_FILES=	easel/devkit/*
+
 OPTIONS_DEFINE=	DOCS EXAMPLES TEST
-TEST_TEST_TARGET=	check
-TEST_USES=	shebangfix perl5
-TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build
 
-DOCFILES=	COPYRIGHT Userguide.pdf
-EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \
-		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \
-		globins4.hmm globins4.out globins4.sto globins45.fa \
-		minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p
+DOCFILES=	Userguide.pdf
+EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
+		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
+		globins4.hmm globins4.sto globins45.fa
+
+TEST_VARS=	use_perl5=build
 
 post-build-TEST-on:	do-test
 
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*
 
 post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
 
 post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
Index: head/biology/hmmer/distinfo
===================================================================
--- head/biology/hmmer/distinfo	(revision 474454)
+++ head/biology/hmmer/distinfo	(revision 474455)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1510218548
-SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536
-SIZE (hmmer-3.1b2.tar.gz) = 5965253
+TIMESTAMP = 1531293655
+SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c
+SIZE (hmmer-3.2.1.tar.gz) = 7670274
Index: head/biology/hmmer/pkg-plist
===================================================================
--- head/biology/hmmer/pkg-plist	(revision 474454)
+++ head/biology/hmmer/pkg-plist	(revision 474455)
@@ -1,70 +1,50 @@
 bin/alimask
 bin/hmmalign
 bin/hmmbuild
-bin/hmmc2
 bin/hmmconvert
 bin/hmmemit
-bin/hmmerfm-exactmatch
 bin/hmmfetch
 bin/hmmlogo
 bin/hmmpgmd
 bin/hmmpress
 bin/hmmscan
 bin/hmmsearch
 bin/hmmsim
 bin/hmmstat
 bin/jackhmmer
 bin/makehmmerdb
 bin/nhmmer
 bin/nhmmscan
 bin/phmmer
-include/cachedb.h
-include/hmmer.h
-include/impl_sse.h
-include/p7_config.h
-include/p7_gbands.h
-include/p7_gmxb.h
-include/p7_gmxchk.h
-include/p7_hmmcache.h
-lib/libhmmer.a
 man/man1/alimask.1.gz
 man/man1/hmmalign.1.gz
 man/man1/hmmbuild.1.gz
 man/man1/hmmconvert.1.gz
 man/man1/hmmemit.1.gz
 man/man1/hmmer.1.gz
 man/man1/hmmfetch.1.gz
 man/man1/hmmlogo.1.gz
 man/man1/hmmpgmd.1.gz
 man/man1/hmmpress.1.gz
 man/man1/hmmscan.1.gz
 man/man1/hmmsearch.1.gz
 man/man1/hmmsim.1.gz
 man/man1/hmmstat.1.gz
 man/man1/jackhmmer.1.gz
 man/man1/makehmmerdb.1.gz
 man/man1/nhmmer.1.gz
 man/man1/nhmmscan.1.gz
 man/man1/phmmer.1.gz
-%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
 %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p