diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile
index 252a5ea5a484..524c59417088 100644
--- a/biology/ncbi-cxx-toolkit/Makefile
+++ b/biology/ncbi-cxx-toolkit/Makefile
@@ -1,52 +1,52 @@
 PORTNAME=	ncbi-cxx-toolkit
 DISTVERSIONPREFIX=	release-
-DISTVERSION=	27.0.0
-PORTREVISION=	1
+DISTVERSION=	28.0.0
 CATEGORIES=	biology science devel
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	NCBI C++ Toolkit
 WWW=		https://ncbi.github.io/cxx-toolkit/
 
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/doc/public/LICENSE
 
 BROKEN_armv6=	platform not defined for FreeBSD arm, see https://github.com/ncbi/ncbi-cxx-toolkit-public/issues/2
 
-LIB_DEPENDS=	libcdd.so:math/cddlib \
+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 61f897e153de..d43fffbfce8d 100644
--- a/biology/ncbi-cxx-toolkit/distinfo
+++ b/biology/ncbi-cxx-toolkit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1687817071
-SHA256 (ncbi-ncbi-cxx-toolkit-public-release-27.0.0_GH0.tar.gz) = c8fb3f99c6fce4f170b381f3a7789c76a2ff1c23c094c9852e2e3de1fdc57277
-SIZE (ncbi-ncbi-cxx-toolkit-public-release-27.0.0_GH0.tar.gz) = 57187775
+TIMESTAMP = 1704429509
+SHA256 (ncbi-ncbi-cxx-toolkit-public-release-28.0.0_GH0.tar.gz) = f0300db41849bbaf690c1dfb9080f3e441fc617a004283acfb2b7b25b32ff885
+SIZE (ncbi-ncbi-cxx-toolkit-public-release-28.0.0_GH0.tar.gz) = 57007980
diff --git a/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app b/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app
deleted file mode 100644
index 8781ac4b7d09..000000000000
--- a/biology/ncbi-cxx-toolkit/files/patch-src_objtools_edit_pubmed__citmatch_Makefile.pubmed__citmatch.app
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/objtools/edit/pubmed_citmatch/Makefile.pubmed_citmatch.app.orig	2023-06-26 23:22:57 UTC
-+++ src/objtools/edit/pubmed_citmatch/Makefile.pubmed_citmatch.app
-@@ -2,7 +2,7 @@
- 
- APP = pubmed_citmatch
- SRC = pubmed_citmatch
--LIB = $(OBJEDIT_LIBS) mlacli mla eutils uilist efetch $(SEQ_LIBS) \
-+LIB = $(OBJEDIT_LIBS) mlacli mla eutils uilist efetch seqset $(SEQ_LIBS) \
-       pubmed medlars pub medline biblio general xser xconnect xutil xncbi
- 
- LIBS = $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS)