diff --git a/biology/gkl/Makefile b/biology/gkl/Makefile
index 7c4c025158c6..128a190d5839 100644
--- a/biology/gkl/Makefile
+++ b/biology/gkl/Makefile
@@ -1,25 +1,24 @@
 PORTNAME=	gkl
-DISTVERSION=	0.8.11-9
-DISTVERSIONSUFFIX=	-g25670d8
+DISTVERSION=	0.9.1
 CATEGORIES=	biology devel
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Accelerated kernel library for genomics
 WWW=		https://github.com/Intel-HLS/GKL
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	gmake:devel/gmake
 LIB_DEPENDS=	libisal.so:devel/isa-l
 
 USES=		cmake:noninja java localbase:ldflags
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	Intel-HLS
 GH_PROJECT=	GKL
 
 BINARY_ALIAS=	make=${GMAKE}
 
 .include <bsd.port.mk>
diff --git a/biology/gkl/distinfo b/biology/gkl/distinfo
index 35c01c063547..d1758a9bcd7a 100644
--- a/biology/gkl/distinfo
+++ b/biology/gkl/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1722788727
-SHA256 (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 743d1eb48c2629454a6dcb98d9adca3aaedfe9c658e6f89e890b03b6e029df61
-SIZE (Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz) = 5310668
+TIMESTAMP = 1755972512
+SHA256 (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 8e32bc3c63013ca6468c65fbbb6af80a433652b640be868d0cb82cb70a919799
+SIZE (Intel-HLS-GKL-0.9.1_GH0.tar.gz) = 5363673
diff --git a/biology/gkl/files/patch-CMakeLists.txt b/biology/gkl/files/patch-CMakeLists.txt
index 2cda423767df..a05193ec57f9 100644
--- a/biology/gkl/files/patch-CMakeLists.txt
+++ b/biology/gkl/files/patch-CMakeLists.txt
@@ -1,11 +1,11 @@
---- CMakeLists.txt.orig	2024-08-04 17:44:32 UTC
+--- CMakeLists.txt.orig	2025-07-07 07:42:12 UTC
 +++ CMakeLists.txt
-@@ -24,6 +24,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native)
+@@ -28,6 +28,8 @@ set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native)
  # add CMakeLists.txt in subdirectories
  set(NATIVE_DIR ${PROJECT_SOURCE_DIR}/src/main/native)
  
 +link_directories(${CMAKE_INSTALL_PREFIX}/lib)
 +
  add_subdirectory("${NATIVE_DIR}/compression")
  add_subdirectory("${NATIVE_DIR}/pairhmm")
  add_subdirectory("${NATIVE_DIR}/utils")
diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h
new file mode 100644
index 000000000000..b47595807911
--- /dev/null
+++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-implementation.h
@@ -0,0 +1,11 @@
+--- src/main/native/pdhmm/pdhmm-implementation.h.orig	2025-08-23 18:25:35 UTC
++++ src/main/native/pdhmm/pdhmm-implementation.h
+@@ -31,7 +31,7 @@
+ #include "avx512_impl.h"
+ #endif
+ 
+-#if defined(__linux__)
++#if defined(__linux__) || defined(__FreeBSD__)
+ #include <omp.h>
+ #endif
+ 
diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc
new file mode 100644
index 000000000000..ebe9e8d41887
--- /dev/null
+++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm-serial.cc
@@ -0,0 +1,11 @@
+--- src/main/native/pdhmm/pdhmm-serial.cc.orig	2025-08-23 18:12:32 UTC
++++ src/main/native/pdhmm/pdhmm-serial.cc
+@@ -24,7 +24,7 @@
+ #include "pdhmm-serial.h"
+ #include "MathUtils.h"
+ #include <cstdio>
+-#if defined(__linux__)
++#if defined(__linux__) || defined(__FreeBSD__)
+ #include <omp.h>
+ #endif
+ 
diff --git a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h
index 4896be46607f..b4afa8fb6791 100644
--- a/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h
+++ b/biology/gkl/files/patch-src_main_native_pdhmm_pdhmm.h
@@ -1,12 +1,12 @@
---- src/main/native/pdhmm/pdhmm.h.orig	2024-08-04 16:31:53 UTC
+--- src/main/native/pdhmm/pdhmm.h.orig	2025-07-07 07:42:12 UTC
 +++ src/main/native/pdhmm/pdhmm.h
 @@ -27,6 +27,9 @@
  #ifdef linux
  #include <omp.h>
  #endif
 +#ifdef __FreeBSD__
 +#include <omp.h>
 +#endif
  
- inline INT_TYPE roundDownToNearestMultipleOf(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; }
+ inline INT_TYPE CONCAT(roundDownToNearestMultipleOf_, SIMD_ENGINE)(INT_TYPE val, INT_TYPE mul) { return (val / mul) * mul; }