Index: head/biology/hmmer/Makefile
===================================================================
--- head/biology/hmmer/Makefile	(revision 456577)
+++ head/biology/hmmer/Makefile	(revision 456578)
@@ -1,43 +1,52 @@
 # Created by: barnhart@genetics.wustl.edu
 # $FreeBSD$
 
 PORTNAME=	hmmer
 PORTVERSION=	3.1b2
 CATEGORIES=	biology
 MASTER_SITES=	http://eddylab.org/software/hmmer3/${PORTVERSION}/
 
 MAINTAINER=	mzaki@niid.go.jp
 COMMENT=	Profile hidden Markov models for biological sequence analysis
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 USES=		gmake
 GNU_CONFIGURE=	yes
 MAKE_ARGS=	V=1
 
 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
 
 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>
+.include <bsd.port.pre.mk>
+
+.if ${MACHINE_CPU:Msse2}
+QMAKE_ARGS+=	UGENE_SSE2_DETECTED=1
+PLIST_SUB+=	SSE2=""
+.else
+PLIST_SUB+=	SSE2="@comment "
+.endif
+
+.include <bsd.port.post.mk>
Index: head/biology/hmmer/pkg-plist
===================================================================
--- head/biology/hmmer/pkg-plist	(revision 456577)
+++ head/biology/hmmer/pkg-plist	(revision 456578)
@@ -1,70 +1,70 @@
 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
+%%SSE2%%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