diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index 6d6ded03e517..4937c94ff19b 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -1,29 +1,29 @@
 PORTNAME=		vsearch
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.28.1
+DISTVERSION=		2.29.0
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Versatile open-source tool for metagenomics
 WWW=		https://github.com/torognes/vsearch
 
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
 ONLY_FOR_ARCHS=		aarch64 amd64 powerpc64le
 ONLY_FOR_ARCHS_REASON=	Explicitly enumerated by upstream developers
 
 USES=		autoreconf ghostscript:build gmake localbase
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	torognes
 GNU_CONFIGURE=	yes
 GNU_CONFIGURE_MANPREFIX=	${PREFIX}/share
 
 PLIST_FILES=	bin/vsearch share/man/man1/vsearch.1.gz
 PORTDOCS=	*
 
 OPTIONS_DEFINE=	DOCS
 OPTIONS_SUB=	yes
 
 .include <bsd.port.mk>
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index f746cec601da..55cfb1fec6ff 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1714566699
-SHA256 (torognes-vsearch-v2.28.1_GH0.tar.gz) = 4f8bf0ad43fef77e573d152b59f55a1f81eb84c22d6545911757e6108f8de21c
-SIZE (torognes-vsearch-v2.28.1_GH0.tar.gz) = 272918
+TIMESTAMP = 1729339584
+SHA256 (torognes-vsearch-v2.29.0_GH0.tar.gz) = 2c5bd0d9b3c2ec8eecd1af06ae11611138d87fdfecfa423ae791d52dccd27e63
+SIZE (torognes-vsearch-v2.29.0_GH0.tar.gz) = 283459
diff --git a/biology/vsearch/files/patch-src_searchcore.cc b/biology/vsearch/files/patch-src_searchcore.cc
new file mode 100644
index 000000000000..84870932c9fd
--- /dev/null
+++ b/biology/vsearch/files/patch-src_searchcore.cc
@@ -0,0 +1,18 @@
+--- src/searchcore.cc.orig	2024-09-26 10:48:55 UTC
++++ src/searchcore.cc
+@@ -239,9 +239,14 @@ auto search_topscores(struct searchinfo_s * si) -> voi
+       if (bitmap)
+         {
+ #ifdef __x86_64__
++	  // Not sure how to enable ssse3 without enabling other
++	  // non-portable features.
++	  // This code is only used rarely, so disable ssse3 for now.
++	  // It won't affect performance much on the whole.
++	  // https://github.com/torognes/vsearch/pull/497
+           if (ssse3_present)
+             {
+-              increment_counters_from_bitmap_ssse3(si->kmers,
++              increment_counters_from_bitmap_sse2(si->kmers,
+                                                    bitmap, indexed_count);
+             }
+           else
diff --git a/biology/vsearch/files/patch-src_sintax.cc b/biology/vsearch/files/patch-src_sintax.cc
new file mode 100644
index 000000000000..c6cd9ec46abb
--- /dev/null
+++ b/biology/vsearch/files/patch-src_sintax.cc
@@ -0,0 +1,18 @@
+--- src/sintax.cc.orig	2024-09-26 10:48:55 UTC
++++ src/sintax.cc
+@@ -289,9 +289,14 @@ auto sintax_search_topscores(struct searchinfo_s * si)
+       if (bitmap)
+         {
+ #ifdef __x86_64__
++	  // Not sure how to enable ssse3 without enabling other
++	  // non-portable features.
++	  // This code is only used rarely, so disable ssse3 for now.
++	  // It won't affect performance much on the whole.
++	  // https://github.com/torognes/vsearch/pull/497
+           if (ssse3_present)
+             {
+-              increment_counters_from_bitmap_ssse3(si->kmers,
++              increment_counters_from_bitmap_sse2(si->kmers,
+                                                    bitmap, indexed_count);
+             }
+           else