debian/changelog

+hyphy (2.5.1+dfsg-3) unstable; urgency=medium
+
+  * Versioned Depends: hyphy-common (= ${source:Version})
+    Closes: #948093
+
+ -- Andreas Tille <tille@debian.org>  Tue, 07 Jan 2020 21:23:52 +0100
+
 hyphy (2.5.1+dfsg-2) unstable; urgency=medium
 
   * Fix installation of NEWS.Debian to enable arch all only builds

debian/control

@@ -19,7 +19,7 @@ Package: hyphy-pt
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         hyphy-common
+         hyphy-common (= ${source:Version})
 Description: Hypothesis testing using Phylogenies (pthreads version)
  HyPhy is an open-source software package for the analysis of genetic
  sequences using techniques in phylogenetics, molecular evolution, and
@@ -37,7 +37,7 @@ Package: hyphy-mpi
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         hyphy-common
+         hyphy-common (= ${source:Version})
 Description: Hypothesis testing using Phylogenies (MPI version)
  HyPhy is an open-source software package for the analysis of genetic
  sequences using techniques in phylogenetics, molecular evolution, and