diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile
index 857094896002..9ac09c497c50 100644
--- a/biology/bowtie2/Makefile
+++ b/biology/bowtie2/Makefile
@@ -1,65 +1,65 @@
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.5.3
+DISTVERSION=		2.5.4
 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
 
 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
 	${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>
diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo
index e9a9a0e0ba4c..c620003fbbce 100644
--- a/biology/bowtie2/distinfo
+++ b/biology/bowtie2/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1705618664
-SHA256 (BenLangmead-bowtie2-v2.5.3_GH0.tar.gz) = 4ac3ece3db011322caab14678b9d80cfc7f75208cdaf0c58b24a6ea0f1a0a60e
-SIZE (BenLangmead-bowtie2-v2.5.3_GH0.tar.gz) = 10635819
+TIMESTAMP = 1716509204
+SHA256 (BenLangmead-bowtie2-v2.5.4_GH0.tar.gz) = 841a6a60111b690c11d1e123cb5c11560b4cd1502b5cee7e394fd50f83e74e13
+SIZE (BenLangmead-bowtie2-v2.5.4_GH0.tar.gz) = 10638569
 SHA256 (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 9874f22afe8a6cd92770aa194df47db3d0963d80ea233a502b0d557f59763eb8
 SIZE (simd-everywhere-simde-no-tests-f6a0b3b_GH0.tar.gz) = 397743