diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile
index 00876a241868..d6bd3efede11 100644
--- a/biology/iqtree/Makefile
+++ b/biology/iqtree/Makefile
@@ -1,37 +1,37 @@
 PORTNAME=	iqtree
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.0.1
+DISTVERSION=	3.1.0
 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
 
-LIB_DEPENDS=	libboost_filesystem.so:devel/boost-libs
+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:29df93e77b7ad159b19e8cdd8150545baa1221ae:iqtree/cmaple
+		iqtree:cmaple:4795b124543c02439722f36cff439bd6517a825b: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 f42a38d7c5f0..869f239e6aec 100644
--- a/biology/iqtree/distinfo
+++ b/biology/iqtree/distinfo
@@ -1,7 +1,7 @@
-TIMESTAMP = 1765767206
-SHA256 (iqtree-iqtree3-v3.0.1_GH0.tar.gz) = 2daff8eaa24faaeac3dee9ac63af9fd7b79cc94cf7031671f0068b051b12c55f
-SIZE (iqtree-iqtree3-v3.0.1_GH0.tar.gz) = 5172154
+TIMESTAMP = 1774135198
+SHA256 (iqtree-iqtree3-v3.1.0_GH0.tar.gz) = 107514383554da08df57732c51cf31ecdaa0fead8de736812e43fcd3fb56bd08
+SIZE (iqtree-iqtree3-v3.1.0_GH0.tar.gz) = 5913669
 SHA256 (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 9bbeaa0f8f35783c1d8dec74df6c93a804dbca808fa04484f9123de4e7258b53
 SIZE (tothuhien-lsd2-c61110f3a4fa05325b45c97b2134792ff9d55d4c_GH0.tar.gz) = 1529381
-SHA256 (iqtree-cmaple-29df93e77b7ad159b19e8cdd8150545baa1221ae_GH0.tar.gz) = f8b5115823614b4c710a13ded1b38b59953c9f3127ced46246d1a4b1db026e37
-SIZE (iqtree-cmaple-29df93e77b7ad159b19e8cdd8150545baa1221ae_GH0.tar.gz) = 4807064
+SHA256 (iqtree-cmaple-4795b124543c02439722f36cff439bd6517a825b_GH0.tar.gz) = 2d3484d4d13374ab04f8fc8b729b1849c2bebe65a825ec6dc22d83840b736215
+SIZE (iqtree-cmaple-4795b124543c02439722f36cff439bd6517a825b_GH0.tar.gz) = 4861543