diff --git a/pkgs/applications/science/biology/cd-hit/default.nix b/pkgs/applications/science/biology/cd-hit/default.nix
index bed562abe23ca2..ba1d6c27ccb17f 100644
--- a/pkgs/applications/science/biology/cd-hit/default.nix
+++ b/pkgs/applications/science/biology/cd-hit/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }:
+{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages, openmp }:
 
 stdenv.mkDerivation rec {
   version = "4.8.1";
@@ -14,8 +14,12 @@ stdenv.mkDerivation rec {
   propagatedBuildInputs = [ perl perlPackages.TextNSP perlPackages.PerlMagick ];
 
   nativeBuildInputs = [ zlib makeWrapper ];
+  buildInputs = lib.optional stdenv.cc.isClang openmp;
 
-  makeFlags = [ "PREFIX=$(out)/bin" ];
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}c++" # remove once https://github.com/weizhongli/cdhit/pull/114 is merged
+    "PREFIX=$(out)/bin"
+  ];
 
   preInstall = "mkdir -p $out/bin";
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 25e0fea7748d0f..2852b79b52beac 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -28941,7 +28941,9 @@ in
 
   bppsuite = callPackage ../applications/science/biology/bppsuite { };
 
-  cd-hit = callPackage ../applications/science/biology/cd-hit { };
+  cd-hit = callPackage ../applications/science/biology/cd-hit {
+    inherit (llvmPackages) openmp;
+  };
 
   cmtk = callPackage ../applications/science/biology/cmtk { };