diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile
index 934943a6c762..6551cf376f95 100644
--- a/biology/ncbi-cxx-toolkit/Makefile
+++ b/biology/ncbi-cxx-toolkit/Makefile
@@ -1,55 +1,55 @@
 PORTNAME=	ncbi-cxx-toolkit
-DISTVERSIONPREFIX=	release-
-DISTVERSION=	28.0.12
+DISTVERSIONPREFIX=	release/
+DISTVERSION=	29.0.1
 CATEGORIES=	biology science devel
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	NCBI C++ Toolkit
 WWW=		https://ncbi.github.io/cxx-toolkit/ \
 		https://github.com/ncbi/ncbi-cxx-toolkit-public
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/doc/public/LICENSE
 
 BROKEN_FreeBSD_15=	compilation fails with clang-15, see https://github.com/ncbi/ncbi-cxx-toolkit-public/issues/13
 BROKEN_armv6=	platform not defined for FreeBSD arm, see https://github.com/ncbi/ncbi-cxx-toolkit-public/issues/2
 BROKEN_armv7=	link fails due to a missing function, see https://github.com/ncbi/ncbi-cxx-toolkit-public/issues/8
 
 LIB_DEPENDS=	libbz2.so:archivers/bzip2 \
 		libcdd.so:math/cddlib \
 		liblmdb.so:databases/lmdb \
 		libpcre.so:devel/pcre \
 		libunwind.so:devel/libunwind \
 		libzstd.so:archivers/zstd
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		compiler:c++17-lang gmake mysql perl5 python shebangfix ssl xorg
 USE_XORG=	x11 xpm
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	ncbi
 GH_PROJECT=	${PORTNAME}-public
 
 SHEBANG_FILES=	src/app/blast/get_species_taxids.sh
 SHEBANG_GLOB=	*.pl *.py
 
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--without-debug --with-dll --without-static \
 		--without-vdb
 
 CONFLICTS_INSTALL=	dakota libxdiff ncbi-blast+ ncbi-toolkit proj \
 			py*-speedtest-cli # bin/blast_formatter bin/speedtest bin/test_regexp lib/libeutils.so lib/libproj.so lib/libxdiff.so
 
 post-install:
 	# strip
 	@${FIND} ${STAGEDIR}${PREFIX}/bin -type f | ${GREP} -v -E '\.(sh|py|pl)$$' | ${XARGS} ${STRIP_CMD}
 	@${FIND} ${STAGEDIR}${PREFIX}/lib -name "*.so" | ${XARGS} ${STRIP_CMD}
 	# remove the conflicting files
 	@${RM} \
 		${STAGEDIR}${PREFIX}/lib/libcdd.so \
 		${STAGEDIR}${PREFIX}/lib/liblmdb.so
 	# autoplist: thousands of files
 	@cd ${STAGEDIR}${PREFIX} && \
 		${FIND} * -type f -or -type l >> ${TMPPLIST}
 
 .include <bsd.port.mk>
diff --git a/biology/ncbi-cxx-toolkit/distinfo b/biology/ncbi-cxx-toolkit/distinfo
index c38bd25b4ad2..20c439054b22 100644
--- a/biology/ncbi-cxx-toolkit/distinfo
+++ b/biology/ncbi-cxx-toolkit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1736230722
-SHA256 (ncbi-ncbi-cxx-toolkit-public-release-28.0.12_GH0.tar.gz) = db8a21ca242480badce126a6cad6ed5a2a8bcf40427fe6ea0dfd1ce6e8755a33
-SIZE (ncbi-ncbi-cxx-toolkit-public-release-28.0.12_GH0.tar.gz) = 57078932
+TIMESTAMP = 1741237344
+SHA256 (ncbi-ncbi-cxx-toolkit-public-release-29.0.1_GH0.tar.gz) = 504ac38917bc9d3a51d17ef504655c017e8353e0e7da145ae6c08a825cb5b77d
+SIZE (ncbi-ncbi-cxx-toolkit-public-release-29.0.1_GH0.tar.gz) = 59674657