diff --git a/biology/python-nexus/Makefile b/biology/python-nexus/Makefile
index f4c08ebdbb7f..06f7e0c6a6c4 100644
--- a/biology/python-nexus/Makefile
+++ b/biology/python-nexus/Makefile
@@ -1,18 +1,21 @@
 PORTNAME=	python-nexus
-PORTVERSION=	1.63
+PORTVERSION=	2.9.0
 CATEGORIES=	biology python
 MASTER_SITES=	PYPI
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Generic nexus file format reader for python
 WWW=		http://simon.net.nz/articles/python-nexus
 
 LICENSE=	BSD3CLAUSE
 #LICENSE_FILE=	${WRKSRC}/LICENSE
 
-USES=		python shebangfix
-SHEBANG_FILES=	nexus/bin/*.py
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}clldutils>=0:devel/py-clldutils@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}termcolor>=0:devel/py-termcolor@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}newick>=0:biology/py-newick@${PY_FLAVOR}
+
+USES=		python
 USE_PYTHON=	autoplist distutils
 
 .include <bsd.port.mk>
diff --git a/biology/python-nexus/distinfo b/biology/python-nexus/distinfo
index cd63640bc1f2..70ddcd274d66 100644
--- a/biology/python-nexus/distinfo
+++ b/biology/python-nexus/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1537606240
-SHA256 (python-nexus-1.63.tar.gz) = 5c9f39bc08a8459078cc65e74f30402df133f8eb06d7acf2c7667e8761657312
-SIZE (python-nexus-1.63.tar.gz) = 37986
+TIMESTAMP = 1706882239
+SHA256 (python-nexus-2.9.0.tar.gz) = 9eea1a0e79dc20b84310a84d4cc90665b1a359a74c17cc0a7602e54156188204
+SIZE (python-nexus-2.9.0.tar.gz) = 34242
diff --git a/biology/python-nexus/files/patch-2to3 b/biology/python-nexus/files/patch-2to3
deleted file mode 100644
index 07cc1ef4371c..000000000000
--- a/biology/python-nexus/files/patch-2to3
+++ /dev/null
@@ -1,19 +0,0 @@
---- nexus/bin/nexuscheck.py.orig	2018-04-10 09:11:00 UTC
-+++ nexus/bin/nexuscheck.py
-@@ -1,6 +1,6 @@
- #!/usr/bin/env python
- import warnings
--from __future__ import print_function
-+
- from nexus import NexusReader, VERSION
- from nexus.checker import checkers
- 
-@@ -44,7 +44,7 @@ if __name__ == '__main__':
-         if len(warned):
-             print("Warnings encountered in reading nexus:")
-             for w in warned:
--                print("\t%s" % w)
-+                print(("\t%s" % w))
-     
-     for checker in checkers:
-         checker(nex, verbose=args.verbose).status()