diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile
index 4d095f50904a..76e54fc007b1 100644
--- a/biology/iqtree/Makefile
+++ b/biology/iqtree/Makefile
@@ -1,37 +1,37 @@
 PORTNAME=	iqtree
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.1.1
+DISTVERSION=	3.1.2
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Efficient phylogenomic software by maximum likelihood
 WWW=		http://www.iqtree.org/
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 ONLY_FOR_ARCHS=	aarch64 amd64
 ONLY_FOR_ARCHS_REASON=	requires 64-bit platform with SSE or NEON
 
 BUILD_DEPENDS=	boost-libs>=0:devel/boost-libs
 
 USES=		cmake eigen:3
 USE_GITHUB=	yes
 GH_PROJECT=	iqtree3
 GH_TUPLE=	tothuhien:lsd2:c61110f3a4fa05325b45c97b2134792ff9d55d4c:tothuhien/lsd2 \
-		iqtree:cmaple:4795b124543c02439722f36cff439bd6517a825b:iqtree/cmaple
+		iqtree:cmaple:3d45b1ab68e2d68a2825bf17a531e22200578cd6: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/distinfo b/biology/iqtree/distinfo
index 8e55721fec90..83ba4b5a0016 100644
--- a/biology/iqtree/distinfo
+++ b/biology/iqtree/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1776629777
-SHA256 (iqtree-iqtree3-v3.1.1_GH0.tar.gz) = f748572d205609040a790df44c7bfa49d8b01ae174e123e927911696befd78c5
-SIZE (iqtree-iqtree3-v3.1.1_GH0.tar.gz) = 5913805
+TIMESTAMP = 1778350394
+SHA256 (iqtree-iqtree3-v3.1.2_GH0.tar.gz) = df85370a2ac74289787226501401ac7db7f085f51c2110d4b829b3f210822160
+SIZE (iqtree-iqtree3-v3.1.2_GH0.tar.gz) = 28742940
 SHA256 (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 9bbeaa0f8f35783c1d8dec74df6c93a804dbca808fa04484f9123de4e7258b53
 SIZE (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 1529381
-SHA256 (iqtree-cmaple-4795b124543c02439722f36cff439bd6517a825b_GH0.tar.gz) = 2d3484d4d13374ab04f8fc8b729b1849c2bebe65a825ec6dc22d83840b736215
-SIZE (iqtree-cmaple-4795b124543c02439722f36cff439bd6517a825b_GH0.tar.gz) = 4861543
+SHA256 (iqtree-cmaple-3d45b1ab68e2d68a2825bf17a531e22200578cd6_GH0.tar.gz) = b8b4d6da2b8571f5a469d1d7154e15135893dc3b5b74876b1131bfdb031a29a9
+SIZE (iqtree-cmaple-3d45b1ab68e2d68a2825bf17a531e22200578cd6_GH0.tar.gz) = 5689506
diff --git a/biology/iqtree/files/patch-terraphast_lib_clamped__uint.cpp b/biology/iqtree/files/patch-terraphast_lib_clamped__uint.cpp
deleted file mode 100644
index 200b2fb455a7..000000000000
--- a/biology/iqtree/files/patch-terraphast_lib_clamped__uint.cpp
+++ /dev/null
@@ -1,17 +0,0 @@
---- terraphast/lib/clamped_uint.cpp.orig	2026-05-05 02:34:53 UTC
-+++ terraphast/lib/clamped_uint.cpp
-@@ -90,14 +90,10 @@ template class checked_uint<true>;
- template class checked_uint<true>;
- 
- // explicitly instantiate template functions
--template bool operator==(checked_uint<false>, checked_uint<false>);
--template bool operator!=(checked_uint<false>, checked_uint<false>);
- template checked_uint<false> operator+(checked_uint<false>, checked_uint<false>);
- template checked_uint<false> operator*(checked_uint<false>, checked_uint<false>);
- template std::ostream& operator<<(std::ostream&, checked_uint<false>);
- 
--template bool operator==(checked_uint<true>, checked_uint<true>);
--template bool operator!=(checked_uint<true>, checked_uint<true>);
- template checked_uint<true> operator+(checked_uint<true>, checked_uint<true>);
- template checked_uint<true> operator*(checked_uint<true>, checked_uint<true>);
- template std::ostream& operator<<(std::ostream&, checked_uint<true>);