diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile
index af11d67a7c5a..00876a241868 100644
--- a/biology/iqtree/Makefile
+++ b/biology/iqtree/Makefile
@@ -1,39 +1,37 @@
 PORTNAME=	iqtree
 DISTVERSIONPREFIX=	v
 DISTVERSION=	3.0.1
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Efficient phylogenomic software by maximum likelihood
 WWW=		http://www.iqtree.org/
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-BROKEN_aarch64=	fails to compile: unrecognized command line option '-msse3'
-BROKEN_powerpc64=	fails to build: GCC version must be at least 4.8!
-NOT_FOR_ARCHS=	armv6 armv7 i386 powerpc
-NOT_FOR_ARCHS_REASON=	32-bit compilation is not supported
+ONLY_FOR_ARCHS=	aarch64 amd64
+ONLY_FOR_ARCHS_REASON=	requires 64-bit platform with SSE or NEON
 
 LIB_DEPENDS=	libboost_filesystem.so:devel/boost-libs
 
 USES=		cmake eigen:3
 USE_GITHUB=	yes
 GH_PROJECT=	iqtree3
 GH_TUPLE=	tothuhien:lsd2:c61110f3a4fa05325b45c97b2134792ff9d55d4c:tothuhien/lsd2 \
 		iqtree:cmaple:29df93e77b7ad159b19e8cdd8150545baa1221ae:iqtree/cmaple
 
 PLIST_FILES=	bin/iqtree
 PORTEXAMPLES=	custom_distributions.txt example.cf example.nex example.phy \
 		models.nex tree.nwk
 
 OPTIONS_DEFINE=	EXAMPLES
 
 do-install:
 	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iqtree3 ${STAGEDIR}${PREFIX}/bin/iqtree
 
 do-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${WRKSRC}/example/* ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/iqtree/files/patch-CMakeLists.txt b/biology/iqtree/files/patch-CMakeLists.txt
new file mode 100644
index 000000000000..e8939e1256d6
--- /dev/null
+++ b/biology/iqtree/files/patch-CMakeLists.txt
@@ -0,0 +1,11 @@
+--- CMakeLists.txt.orig	2026-02-11 08:46:02 UTC
++++ CMakeLists.txt
+@@ -229,7 +229,7 @@ elseif (UNIX AND NOT APPLE)  # Unix and Linux
+       OUTPUT_VARIABLE OS_NATIVE_ARCHITECTURE
+       OUTPUT_STRIP_TRAILING_WHITESPACE
+     )
+-    if(OS_NATIVE_ARCHITECTURE STREQUAL "aarch64")
++    if(OS_NATIVE_ARCHITECTURE STREQUAL "aarch64" OR OS_NATIVE_ARCHITECTURE STREQUAL "arm64")
+         message("Unix/Linux ARM64 DETECTED!")
+ 	    set (__ARM_NEON "TRUE")
+ 		set (NEON 1)