diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index 9ac09c497c50..90c2e22f7663 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,65 +1,76 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.5.4
+DISTVERSION=		2.5.5
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Ultrafast, memory-efficient short read aligner
 WWW=		https://github.com/BenLangmead/bowtie2
 
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 ONLY_FOR_ARCHS=	aarch64 amd64 powerpc64 powerpc64le
 ONLY_FOR_ARCHS_REASON=	Requires a 64-bit processor
 
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		gmake localbase:ldflags perl5 python shebangfix
 USE_PERL5=	run
 USE_GITHUB=	yes
 
 SHEBANG_FILES=	bowtie2 bowtie2-build bowtie2-inspect \
 		scripts/bowtie2-hbb.sh scripts/*.pl
 GH_ACCOUNT=	BenLangmead
 GH_TUPLE=	simd-everywhere:simde-no-tests:f6a0b3b:simde
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
 SUB_FILES=	bowtie2-test
 
 .include <bsd.port.options.mk>
 
 .if ${ARCH} != amd64
 post-extract:
 	(cd ${WRKSRC_simde}; \
 		${COPYTREE_SHARE} . ${WRKSRC}/third_party/simde/)
 
 MAKE_ENV=	POPCNT_CAPABILITY=0
 .endif
 
+.include <bsd.port.pre.mk>
+
+.if ${ARCH} == amd64
+PLIST_SUB+=	X86_64_ONLY=""
+.else
+PLIST_SUB+=	X86_64_ONLY="@comment "
+.endif
+
 pre-configure:
 	@${REINPLACE_CMD} \
 		-e 's|^RELEASE_FLAGS|# RELEASE_FLAGS|' \
 		-e 's|tbbmalloc_proxy|tbbmalloc|' \
 		${WRKSRC}/Makefile
 
 post-install:
 	@${MKDIR} ${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_PROGRAM} \
 		${WRKSRC}/bowtie2*-s \
 		${WRKSRC}/bowtie2*-l \
 		${STAGEDIR}${PREFIX}/bin
+.if ${ARCH} == amd64
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*256
+.endif
 	${INSTALL_SCRIPT} \
 		${WRKSRC}/scripts/*.sh \
 		${WRKSRC}/scripts/*.pl \
 		${STAGEDIR}${DATADIR}/scripts
 	${INSTALL_SCRIPT} ${WRKDIR}/bowtie2-test ${STAGEDIR}${PREFIX}/bin
 
 post-install-DOCS-on:
 	(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
 
 post-install-EXAMPLES-on:
 	(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index c620003fbbce..367170fef258 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1716509204
-SHA256 (BenLangmead-bowtie2-v2.5.4_GH0.tar.gz) = 841a6a60111b690c11d1e123cb5c11560b4cd1502b5cee7e394fd50f83e74e13
-SIZE (BenLangmead-bowtie2-v2.5.4_GH0.tar.gz) = 10638569
+TIMESTAMP = 1771903062
+SHA256 (BenLangmead-bowtie2-v2.5.5_GH0.tar.gz) = e38d1833ec235ca27fa57589d32d897c9addf87085b7cb7bc978662954662da2
+SIZE (BenLangmead-bowtie2-v2.5.5_GH0.tar.gz) = 10645909
 SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8
 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743
diff --git a/biology/bowtie2/pkg-plist b/biology/bowtie2/pkg-plist
index e79354fbbb9f..7ff259d16825 100644
--- a/biology/bowtie2/pkg-plist
+++ b/biology/bowtie2/pkg-plist
@@ -1,67 +1,69 @@
 bin/bowtie2
 bin/bowtie2-align-l
+%%X86_64_ONLY%%bin/bowtie2-align-l-v256
 bin/bowtie2-align-s
+%%X86_64_ONLY%%bin/bowtie2-align-s-v256
 bin/bowtie2-build
 bin/bowtie2-build-l
 bin/bowtie2-build-s
 bin/bowtie2-inspect
 bin/bowtie2-inspect-l
 bin/bowtie2-inspect-s
 bin/bowtie2-test
 %%DATADIR%%/scripts/bowtie2-hbb.sh
 %%DATADIR%%/scripts/convert_quals.pl
 %%DATADIR%%/scripts/gen_2b_occ_lookup.pl
 %%DATADIR%%/scripts/gen_occ_lookup.pl
 %%DATADIR%%/scripts/gen_solqual_lookup.pl
 %%DATADIR%%/scripts/infer_fraglen.pl
 %%DATADIR%%/scripts/make_a_thaliana_tair.sh
 %%DATADIR%%/scripts/make_b_taurus_UMD3.sh
 %%DATADIR%%/scripts/make_c_elegans.sh
 %%DATADIR%%/scripts/make_canFam2.sh
 %%DATADIR%%/scripts/make_d_melanogaster.sh
 %%DATADIR%%/scripts/make_e_coli.sh
 %%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh
 %%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh
 %%DATADIR%%/scripts/make_hg18.sh
 %%DATADIR%%/scripts/make_hg19.sh
 %%DATADIR%%/scripts/make_m_musculus_ncbi37.sh
 %%DATADIR%%/scripts/make_mm10.sh
 %%DATADIR%%/scripts/make_mm9.sh
 %%DATADIR%%/scripts/make_rn4.sh
 %%DATADIR%%/scripts/make_s_cerevisiae.sh
 %%PORTDOCS%%%%DOCSDIR%%/README
 %%PORTDOCS%%%%DOCSDIR%%/images/bowtie_logo.png
 %%PORTDOCS%%%%DOCSDIR%%/images/osi-certified.gif
 %%PORTDOCS%%%%DOCSDIR%%/images/sflogo.png
 %%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png
 %%PORTDOCS%%%%DOCSDIR%%/manual.html
 %%PORTDOCS%%%%DOCSDIR%%/release.txt
 %%PORTDOCS%%%%DOCSDIR%%/style.css
 %%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/index.html
 %%PORTDOCS%%%%DOCSDIR%%/website/index.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/news.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml
 %%PORTDOCS%%%%DOCSDIR%%/website/push.sh
 %%PORTDOCS%%%%DOCSDIR%%/website/push_images.sh
 %%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi
 %%PORTDOCS%%%%DOCSDIR%%/website/top.ssi
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.1.bt2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.2.bt2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.3.bt2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.4.bt2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.1.bt2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.2.bt2
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/combined_reads.bam
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/conversion_utilities.sh
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/longreads.fq
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_1.fq
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_2.fq
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/simulate.pl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reference/lambda_virus.fa