--- last-align.orig/src/mcf_simd.hh
+++ last-align/src/mcf_simd.hh
@@ -4,38 +4,36 @@
 #ifndef MCF_SIMD_HH
 #define MCF_SIMD_HH
 
-#include <immintrin.h>
+#include "../debian/include/simde/x86/avx2.h"
 
 namespace mcf {
 
-#if defined __AVX2__
-
-typedef __m256i SimdInt;
+typedef simde__m256i SimdInt;
 
 const int simdBytes = 32;
 
 static inline SimdInt simdZero() {
-  return _mm256_setzero_si256();
+  return simde_mm256_setzero_si256();
 }
 
 static inline SimdInt simdOnes() {
-  return _mm256_set1_epi32(-1);
+  return simde_mm256_set1_epi32(-1);
 }
 
 static inline SimdInt simdLoad(const void *p) {
-  return _mm256_loadu_si256((const SimdInt *)p);
+  return simde_mm256_loadu_si256((const SimdInt *)p);
 }
 
 static inline void simdStore(void *p, SimdInt x) {
-  _mm256_storeu_si256((SimdInt *)p, x);
+  simde_mm256_storeu_si256((SimdInt *)p, x);
 }
 
 static inline SimdInt simdOr(SimdInt x, SimdInt y) {
-  return _mm256_or_si256(x, y);
+  return simde_mm256_or_si256(x, y);
 }
 
 static inline SimdInt simdBlend(SimdInt x, SimdInt y, SimdInt mask) {
-  return _mm256_blendv_epi8(x, y, mask);
+  return simde_mm256_blendv_epi8(x, y, mask);
 }
 
 const int simdLen = 8;
@@ -43,14 +41,14 @@
 
 static inline SimdInt simdSet(int i7, int i6, int i5, int i4,
 			      int i3, int i2, int i1, int i0) {
-  return _mm256_set_epi32(i7, i6, i5, i4, i3, i2, i1, i0);
+  return simde_mm256_set_epi32(i7, i6, i5, i4, i3, i2, i1, i0);
 }
 
 static inline SimdInt simdSet2(short iF, short iE, short iD, short iC,
 			       short iB, short iA, short i9, short i8,
 			       short i7, short i6, short i5, short i4,
 			       short i3, short i2, short i1, short i0) {
-  return _mm256_set_epi16(iF, iE, iD, iC, iB, iA, i9, i8,
+  return simde_mm256_set_epi16(iF, iE, iD, iC, iB, iA, i9, i8,
 			  i7, i6, i5, i4, i3, i2, i1, i0);
 }
 
@@ -62,265 +60,108 @@
 			       char iB, char iA, char i9, char i8,
 			       char i7, char i6, char i5, char i4,
 			       char i3, char i2, char i1, char i0) {
-  return _mm256_set_epi8(jF, jE, jD, jC, jB, jA, j9, j8,
+  return simde_mm256_set_epi8(jF, jE, jD, jC, jB, jA, j9, j8,
 			 j7, j6, j5, j4, j3, j2, j1, j0,
 			 iF, iE, iD, iC, iB, iA, i9, i8,
 			 i7, i6, i5, i4, i3, i2, i1, i0);
 }
 
 static inline SimdInt simdFill(int x) {
-  return _mm256_set1_epi32(x);
+  return simde_mm256_set1_epi32(x);
 }
 
 static inline SimdInt simdFill2(short x) {
-  return _mm256_set1_epi16(x);
+  return simde_mm256_set1_epi16(x);
 }
 
 static inline SimdInt simdFill1(char x) {
-  return _mm256_set1_epi8(x);
+  return simde_mm256_set1_epi8(x);
 }
 
 static inline SimdInt simdEq1(SimdInt x, SimdInt y) {
-  return _mm256_cmpeq_epi8(x, y);
+  return simde_mm256_cmpeq_epi8(x, y);
 }
 
 static inline SimdInt simdGt(SimdInt x, SimdInt y) {
-  return _mm256_cmpgt_epi32(x, y);
+  return simde_mm256_cmpgt_epi32(x, y);
 }
 
 static inline SimdInt simdGt2(SimdInt x, SimdInt y) {
-  return _mm256_cmpgt_epi16(x, y);
+  return simde_mm256_cmpgt_epi16(x, y);
 }
 
 static inline SimdInt simdAdd(SimdInt x, SimdInt y) {
-  return _mm256_add_epi32(x, y);
+  return simde_mm256_add_epi32(x, y);
 }
 
 static inline SimdInt simdAdd2(SimdInt x, SimdInt y) {
-  return _mm256_add_epi16(x, y);
+  return simde_mm256_add_epi16(x, y);
 }
 
 static inline SimdInt simdAdd1(SimdInt x, SimdInt y) {
-  return _mm256_add_epi8(x, y);
+  return simde_mm256_add_epi8(x, y);
 }
 
 static inline SimdInt simdAdds1(SimdInt x, SimdInt y) {
-  return _mm256_adds_epu8(x, y);
+  return simde_mm256_adds_epu8(x, y);
 }
 
 static inline SimdInt simdSub(SimdInt x, SimdInt y) {
-  return _mm256_sub_epi32(x, y);
+  return simde_mm256_sub_epi32(x, y);
 }
 
 static inline SimdInt simdSub2(SimdInt x, SimdInt y) {
-  return _mm256_sub_epi16(x, y);
+  return simde_mm256_sub_epi16(x, y);
 }
 
 static inline SimdInt simdSub1(SimdInt x, SimdInt y) {
-  return _mm256_sub_epi8(x, y);
+  return simde_mm256_sub_epi8(x, y);
 }
 
 static inline SimdInt simdLeft(SimdInt x, int bits) {
-  return _mm256_slli_epi32(x, bits);
+  return simde_mm256_slli_epi32(x, bits);
 }
 
 static inline SimdInt simdMax(SimdInt x, SimdInt y) {
-  return _mm256_max_epi32(x, y);
+  return simde_mm256_max_epi32(x, y);
 }
 
 static inline SimdInt simdMax2(SimdInt x, SimdInt y) {
-  return _mm256_max_epi16(x, y);
+  return simde_mm256_max_epi16(x, y);
 }
 
 static inline SimdInt simdMin1(SimdInt x, SimdInt y) {
-  return _mm256_min_epu8(x, y);
+  return simde_mm256_min_epu8(x, y);
 }
 
 static inline int simdHorizontalMax(SimdInt x) {
-  __m128i z = _mm256_castsi256_si128(x);
-  z = _mm_max_epi32(z, _mm256_extracti128_si256(x, 1));
-  z = _mm_max_epi32(z, _mm_shuffle_epi32(z, 0x4E));
-  z = _mm_max_epi32(z, _mm_shuffle_epi32(z, 0xB1));
-  return _mm_cvtsi128_si32(z);
+  simde__m128i z = simde_mm256_castsi256_si128(x);
+  z = simde_mm_max_epi32(z, simde_mm256_extracti128_si256(x, 1));
+  z = simde_mm_max_epi32(z, simde_mm_shuffle_epi32(z, 0x4E));
+  z = simde_mm_max_epi32(z, simde_mm_shuffle_epi32(z, 0xB1));
+  return simde_mm_cvtsi128_si32(z);
 }
 
 static inline int simdHorizontalMax2(SimdInt x) {
-  __m128i z = _mm256_castsi256_si128(x);
-  z = _mm_max_epi16(z, _mm256_extracti128_si256(x, 1));
-  z = _mm_sub_epi16(_mm_set1_epi16(32767), z);
-  z = _mm_minpos_epu16(z);
-  return 32767 - _mm_extract_epi16(z, 0);
+  simde__m128i z = simde_mm256_castsi256_si128(x);
+  z = simde_mm_max_epi16(z, simde_mm256_extracti128_si256(x, 1));
+  z = simde_mm_sub_epi16(simde_mm_set1_epi16(32767), z);
+  z = simde_mm_minpos_epu16(z);
+  return 32767 - simde_mm_extract_epi16(z, 0);
 }
 
 static inline int simdHorizontalMin1(SimdInt x) {
-  __m128i z = _mm256_castsi256_si128(x);
-  z = _mm_min_epu8(z, _mm256_extracti128_si256(x, 1));
-  z = _mm_min_epu8(z, _mm_srli_epi16(z, 8));
-  z = _mm_minpos_epu16(z);
-  return _mm_extract_epi16(z, 0);
+  simde__m128i z = simde_mm256_castsi256_si128(x);
+  z = simde_mm_min_epu8(z, simde_mm256_extracti128_si256(x, 1));
+  z = simde_mm_min_epu8(z, simde_mm_srli_epi16(z, 8));
+  z = simde_mm_minpos_epu16(z);
+  return simde_mm_extract_epi16(z, 0);
 }
 
 static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
-  return _mm256_shuffle_epi8(items, choices);
-}
-
-#elif defined __SSE4_1__
-
-typedef __m128i SimdInt;
-
-const int simdBytes = 16;
-
-static inline SimdInt simdZero() {
-  return _mm_setzero_si128();
-}
-
-static inline SimdInt simdOnes() {
-  return _mm_set1_epi32(-1);
-}
-
-static inline SimdInt simdLoad(const void *p) {
-  return _mm_loadu_si128((const SimdInt *)p);
-}
-
-static inline void simdStore(void *p, SimdInt x) {
-  _mm_storeu_si128((SimdInt *)p, x);
-}
-
-static inline SimdInt simdOr(SimdInt x, SimdInt y) {
-  return _mm_or_si128(x, y);
-}
-
-static inline SimdInt simdBlend(SimdInt x, SimdInt y, SimdInt mask) {
-  return _mm_blendv_epi8(x, y, mask);  // SSE4.1
-}
-
-const int simdLen = 4;
-const int simdLen2 = 8;
-
-static inline SimdInt simdSet(int i3, int i2, int i1, int i0) {
-  return _mm_set_epi32(i3, i2, i1, i0);
+  return simde_mm256_shuffle_epi8(items, choices);
 }
 
-static inline SimdInt simdSet2(short i7, short i6, short i5, short i4,
-			       short i3, short i2, short i1, short i0) {
-  return _mm_set_epi16(i7, i6, i5, i4, i3, i2, i1, i0);
-}
-
-static inline SimdInt simdSet1(char iF, char iE, char iD, char iC,
-			       char iB, char iA, char i9, char i8,
-			       char i7, char i6, char i5, char i4,
-			       char i3, char i2, char i1, char i0) {
-  return _mm_set_epi8(iF, iE, iD, iC, iB, iA, i9, i8,
-		      i7, i6, i5, i4, i3, i2, i1, i0);
-}
-
-static inline SimdInt simdFill(int x) {
-  return _mm_set1_epi32(x);
-}
-
-static inline SimdInt simdFill2(short x) {
-  return _mm_set1_epi16(x);
-}
-
-static inline SimdInt simdFill1(char x) {
-  return _mm_set1_epi8(x);
-}
-
-static inline SimdInt simdEq1(SimdInt x, SimdInt y) {
-  return _mm_cmpeq_epi8(x, y);
-}
-
-static inline SimdInt simdGt(SimdInt x, SimdInt y) {
-  return _mm_cmpgt_epi32(x, y);
-}
-
-static inline SimdInt simdGt2(SimdInt x, SimdInt y) {
-  return _mm_cmpgt_epi16(x, y);
-}
-
-static inline SimdInt simdAdd(SimdInt x, SimdInt y) {
-  return _mm_add_epi32(x, y);
-}
-
-static inline SimdInt simdAdd2(SimdInt x, SimdInt y) {
-  return _mm_add_epi16(x, y);
-}
-
-static inline SimdInt simdAdd1(SimdInt x, SimdInt y) {
-  return _mm_add_epi8(x, y);
-}
-
-static inline SimdInt simdAdds1(SimdInt x, SimdInt y) {
-  return _mm_adds_epu8(x, y);
-}
-
-static inline SimdInt simdSub(SimdInt x, SimdInt y) {
-  return _mm_sub_epi32(x, y);
-}
-
-static inline SimdInt simdSub2(SimdInt x, SimdInt y) {
-  return _mm_sub_epi16(x, y);
-}
-
-static inline SimdInt simdSub1(SimdInt x, SimdInt y) {
-  return _mm_sub_epi8(x, y);
-}
-
-static inline SimdInt simdLeft(SimdInt x, int bits) {
-  return _mm_slli_epi32(x, bits);
-}
-
-static inline SimdInt simdMax(SimdInt x, SimdInt y) {
-  return _mm_max_epi32(x, y);  // SSE4.1
-}
-
-static inline SimdInt simdMax2(SimdInt x, SimdInt y) {
-  return _mm_max_epi16(x, y);
-}
-
-static inline SimdInt simdMin1(SimdInt x, SimdInt y) {
-  return _mm_min_epu8(x, y);
-}
-
-static inline int simdHorizontalMax(SimdInt x) {
-  x = simdMax(x, _mm_shuffle_epi32(x, 0x4E));
-  x = simdMax(x, _mm_shuffle_epi32(x, 0xB1));
-  return _mm_cvtsi128_si32(x);
-}
-
-static inline int simdHorizontalMax2(SimdInt x) {
-  x = simdSub2(simdFill2(32767), x);
-  x = _mm_minpos_epu16(x);  // SSE4.1
-  return 32767 - _mm_extract_epi16(x, 0);
-}
-
-static inline int simdHorizontalMin1(SimdInt x) {
-  x = _mm_min_epu8(x, _mm_srli_epi16(x, 8));
-  x = _mm_minpos_epu16(x);  // SSE4.1
-  return _mm_extract_epi16(x, 0);
-}
-
-static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
-  return _mm_shuffle_epi8(items, choices);
-}
-
-#else
-
-typedef int SimdInt;
-const int simdLen = 1;
-static inline int simdSet(int x) { return x; }
-static inline int simdFill(int x) { return x; }
-static inline int simdLoad(const int *p) { return *p; }
-static inline void simdStore(int *p, int x) { *p = x; }
-static inline int simdGt(int x, int y) { return x > y; }
-static inline int simdAdd(int x, int y) { return x + y; }
-static inline int simdSub(int x, int y) { return x - y; }
-static inline int simdMax(int x, int y) { return x > y ? x : y; }
-static inline int simdBlend(int x, int y, int mask) { return mask ? y : x; }
-static inline int simdHorizontalMax(int a) { return a; }
-
-#endif
-
 }
 
 #endif
--- last-align.orig/src/GappedXdropAligner.cc
+++ last-align/src/GappedXdropAligner.cc
@@ -141,17 +141,13 @@
     if (isAffine) {
       for (int i = 0; i < numCells; i += simdLen) {
 	SimdInt s = simdSet(
-#ifdef __SSE4_1__
-#ifdef __AVX2__
 			    s1[7][s2[7]],
 			    s1[6][s2[6]],
 			    s1[5][s2[5]],
 			    s1[4][s2[4]],
-#endif
 			    s1[3][s2[3]],
 			    s1[2][s2[2]],
 			    s1[1][s2[1]],
-#endif
 			    s1[0][s2[0]]);
 	SimdInt x = simdLoad(x2+i);
 	SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);
--- last-align.orig/src/GappedXdropAlignerPssm.cc
+++ last-align/src/GappedXdropAlignerPssm.cc
@@ -92,17 +92,13 @@
     if (isAffine) {
       for (int i = 0; i < numCells; i += simdLen) {
 	SimdInt s = simdSet(
-#ifdef __SSE4_1__
-#ifdef __AVX2__
 			    s2[-7][s1[7]],
 			    s2[-6][s1[6]],
 			    s2[-5][s1[5]],
 			    s2[-4][s1[4]],
-#endif
 			    s2[-3][s1[3]],
 			    s2[-2][s1[2]],
 			    s2[-1][s1[1]],
-#endif
 			    s2[-0][s1[0]]);
 	SimdInt x = simdLoad(x2+i);
 	SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);
--- last-align.orig/makefile
+++ last-align/makefile
@@ -2,15 +2,24 @@
 all:
 	@cd src && $(MAKE) CXXFLAGS="$(CXXFLAGS)"
 
-progs = src/lastdb src/lastal src/last-split src/last-merge-batches	\
-src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8
+SFX :=
+progs = src/lastdb$(SFX) src/lastal$(SFX) src/last-split$(SFX) \
+	src/last-merge-batches$(SFX) src/last-pair-probs$(SFX) src/lastdb8$(SFX) \
+	src/lastal8$(SFX) src/last-split8$(SFX)
 
 prefix = /usr/local
 exec_prefix = $(prefix)
 bindir = $(exec_prefix)/bin
+libexecdir = $(exec_prefix)/libexec
+
 install: all
 	mkdir -p $(bindir)
-	cp $(progs) scripts/* $(bindir)
+	cp scripts/* $(bindir)
+ifeq (,$(SFX))
+	cp $(progs) $(bindir)
+else
+	cp $(progs) $(libexecdir)
+endif
 
 clean:
 	@cd src && $(MAKE) clean
--- last-align.orig/src/makefile
+++ last-align/src/makefile
@@ -57,8 +57,10 @@
 
 MBOBJ = last-merge-batches.o
 
-ALL = lastdb lastal last-split last-merge-batches last-pair-probs	\
-lastdb8 lastal8 last-split8
+SFX :=
+
+ALL = lastdb$(SFX) lastal$(SFX) last-split$(SFX) last-merge-batches$(SFX) \
+      last-pair-probs$(SFX) lastdb8$(SFX) lastal8$(SFX) last-split8$(SFX)
 
 indexObj8 = $(indexObj4:.o=.o8)
 alignObj8 = $(alignObj4:.o=.o8)
@@ -67,33 +69,33 @@
 all: $(ALL)
 
 indexAllObj4 = $(indexObj0) $(indexObj4)
-lastdb: $(indexAllObj4)
+lastdb$(SFX): $(indexAllObj4)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj4) -lz
 
 indexAllObj8 = $(indexObj0) $(indexObj8)
-lastdb8: $(indexAllObj8)
+lastdb8$(SFX): $(indexAllObj8)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(indexAllObj8) -lz
 
 alignAllObj4 = $(alignObj0) $(alignObj4)
-lastal: $(alignAllObj4)
+lastal$(SFX): $(alignAllObj4)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj4) -lz
 
 alignAllObj8 = $(alignObj0) $(alignObj8)
-lastal8: $(alignAllObj8)
+lastal8$(SFX): $(alignAllObj8)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(alignAllObj8) -lz
 
 splitAllObj4 = $(splitObj0) $(splitObj4)
-last-split: $(splitAllObj4)
+last-split$(SFX): $(splitAllObj4)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj4)
 
 splitAllObj8 = $(splitObj0) $(splitObj8)
-last-split8: $(splitAllObj8)
+last-split8$(SFX): $(splitAllObj8)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(splitAllObj8)
 
-last-pair-probs: $(PPOBJ)
+last-pair-probs$(SFX): $(PPOBJ)
 	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ $(PPOBJ) -lz
 
-last-merge-batches: $(MBOBJ)
+last-merge-batches$(SFX): $(MBOBJ)
 	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ $(MBOBJ)
 
 .SUFFIXES:
--- last-align.orig/src/GappedXdropAlignerDna.cc
+++ last-align/src/GappedXdropAlignerDna.cc
@@ -41,12 +41,10 @@
 
   const SimdInt scorer4x4 =
     simdSet1(
-#ifdef __AVX2__
 		 scorer[3][3], scorer[3][2], scorer[3][1], scorer[3][0],
 		 scorer[2][3], scorer[2][2], scorer[2][1], scorer[2][0],
 		 scorer[1][3], scorer[1][2], scorer[1][1], scorer[1][0],
 		 scorer[0][3], scorer[0][2], scorer[0][1], scorer[0][0],
-#endif
 		 scorer[3][3], scorer[3][2], scorer[3][1], scorer[3][0],
 		 scorer[2][3], scorer[2][2], scorer[2][1], scorer[2][0],
 		 scorer[1][3], scorer[1][2], scorer[1][1], scorer[1][0],
@@ -125,8 +123,6 @@
 
       for (int i = 0; i < numCells; i += simdBytes) {
 	SimdInt s = simdSet1(
-#ifdef __SSE4_1__
-#ifdef __AVX2__
 			     scorer[s1[31]][s2[31]],
 			     scorer[s1[30]][s2[30]],
 			     scorer[s1[29]][s2[29]],
@@ -143,7 +139,6 @@
 			     scorer[s1[18]][s2[18]],
 			     scorer[s1[17]][s2[17]],
 			     scorer[s1[16]][s2[16]],
-#endif
 			     scorer[s1[15]][s2[15]],
 			     scorer[s1[14]][s2[14]],
 			     scorer[s1[13]][s2[13]],
@@ -159,7 +154,6 @@
 			     scorer[s1[3]][s2[3]],
 			     scorer[s1[2]][s2[2]],
 			     scorer[s1[1]][s2[1]],
-#endif
 			     scorer[s1[0]][s2[0]]);
 
 	SimdInt x = simdAdds1(simdLoad(x2+i), mScoreRise12);
