diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile
index 5752c102500c..fc48fb410933 100644
--- a/biology/iqtree/Makefile
+++ b/biology/iqtree/Makefile
@@ -1,39 +1,39 @@
 PORTNAME=	iqtree
-DISTVERSIONPREFIX=	v
-DISTVERSION=	2.3.2
+DISTVERSIONPREFIX=	v.
+DISTVERSION=	2.3.4
 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_armv6=	fails to compile: unrecognized command line options '-m32' and '-msse3'
 BROKEN_armv7=	fails to compile: unrecognized command line options '-m32' and '-msse3'
 BROKEN_i386=	ld: error: unable to find library -latomic (see bug 230888)
 BROKEN_powerpc64=	fails to build: GCC version must be at least 4.8!
 
 LIB_DEPENDS=	libboost_filesystem.so:devel/boost-libs
 
 USES=		cmake eigen:3
 USE_GITHUB=	yes
 GH_PROJECT=	iqtree2
 GH_TUPLE=	tothuhien:lsd2:26ba127:iqtree2/lsd2
 
 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}/iqtree2 ${STAGEDIR}${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/distinfo b/biology/iqtree/distinfo
index 4b5ff2269f5f..ebd56f55dff4 100644
--- a/biology/iqtree/distinfo
+++ b/biology/iqtree/distinfo
@@ -1,5 +1,5 @@
-TIMESTAMP = 1713099860
-SHA256 (iqtree-iqtree2-v2.3.2_GH0.tar.gz) = c1f97b5fba459561739f4213e7014f29049e070f0cbe2a20473279b372e3c12e
-SIZE (iqtree-iqtree2-v2.3.2_GH0.tar.gz) = 6161544
+TIMESTAMP = 1715872647
+SHA256 (iqtree-iqtree2-v.2.3.4_GH0.tar.gz) = 35bdac31c5795e5c72e532c2a311aa8266c9d40e7d668ee84c3b6e975af318da
+SIZE (iqtree-iqtree2-v.2.3.4_GH0.tar.gz) = 6568572
 SHA256 (tothuhien-lsd2-26ba127_GH0.tar.gz) = 63226da0e326d9fc47c54e8e380d48e51e923ccc25bd7f286d49b9f49028d1c4
 SIZE (tothuhien-lsd2-26ba127_GH0.tar.gz) = 1079490
diff --git a/biology/iqtree/files/patch-CMakeLists.txt b/biology/iqtree/files/patch-CMakeLists.txt
deleted file mode 100644
index d52f30670d91..000000000000
--- a/biology/iqtree/files/patch-CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
---- CMakeLists.txt.orig	2023-09-05 01:20:58 UTC
-+++ CMakeLists.txt
-@@ -398,7 +398,7 @@ if (NOT IQTREE_FLAGS MATCHES "single")
-     	else()
-         	link_directories(${PROJECT_SOURCE_DIR}/libmac)
-         endif()	
--    elseif (WIN32 OR UNIX)
-+    elseif (WIN32 OR UNIX AND NOT ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD")
-         if (BINARY32)
-             link_directories(${PROJECT_SOURCE_DIR}/lib32)
-         else()