diff --git a/pkgs/applications/science/biology/mmseqs2/default.nix b/pkgs/applications/science/biology/mmseqs2/default.nix
new file mode 100644
index 000000000000..253f4a43a81c
--- /dev/null
+++ b/pkgs/applications/science/biology/mmseqs2/default.nix
@@ -0,0 +1,50 @@
+{ lib
+, stdenv
+, fetchFromGitHub
+, cmake
+, xxd
+, perl
+, installShellFiles
+, enableAvx2 ? stdenv.hostPlatform.avx2Support
+, enableSse4_1 ? stdenv.hostPlatform.sse4_1Support
+, enableMpi ? false
+, mpi
+, openmp
+, zlib
+, bzip2
+}:
+
+stdenv.mkDerivation rec {
+  pname = "mmseqs2";
+  version = "14-7e284";
+
+  src = fetchFromGitHub {
+    owner = "soedinglab";
+    repo = pname;
+    rev = version;
+    sha256 = "sha256-pVryZGblgMEqJl5M20CHxav269yGY6Y4ci+Gxt6SHOU=";
+  };
+
+  nativeBuildInputs = [ cmake xxd perl installShellFiles ];
+  cmakeFlags =
+    lib.optional enableAvx2 "-DHAVE_AVX2=1"
+    ++ lib.optional enableSse4_1 "-DHAVE_SSE4_1=1"
+    ++ lib.optional enableMpi "-DHAVE_MPI=1";
+
+  buildInputs =
+    lib.optionals stdenv.cc.isClang [ openmp zlib bzip2 ]
+    ++ lib.optional enableMpi mpi;
+
+  postInstall = ''
+    installShellCompletion --bash --cmd mmseqs $out/util/bash-completion.sh
+    rm -r $out/util/
+  '';
+
+  meta = with lib; {
+    description = "Ultra fast and sensitive sequence search and clustering suite";
+    homepage = "https://mmseqs.com/";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 762fb599df35..c11c214d5b1a 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -35200,6 +35200,10 @@ with pkgs;
 
   minimap2 = callPackage ../applications/science/biology/minimap2 { };
 
+  mmseqs2 = callPackage ../applications/science/biology/mmseqs2 {
+    inherit (llvmPackages) openmp;
+  };
+
   mosdepth = callPackage ../applications/science/biology/mosdepth { };
 
   niftyreg = callPackage ../applications/science/biology/niftyreg { };