diff --git a/science/raxml/Portfile b/science/raxml/Portfile
index 9945f96986e82..1c520ce88efb3 100644
--- a/science/raxml/Portfile
+++ b/science/raxml/Portfile
@@ -3,9 +3,11 @@
 PortSystem          1.0
 PortGroup           github 1.0
 PortGroup           mpi 1.0
+PortGroup           xcode_workaround 1.0
+PortGroup           makefile 1.0
 
 github.setup        stamatak standard-RAxML 7.7.6 v
-revision            1
+revision            2
 checksums           sha256  7562b307bc50e38162f104271793a1c8f98f866c2342bea21afe6df6a982fd82 \
                     rmd160  da76d6623515b7d8f78a69aaf4eec713508789af
 name                raxml
@@ -22,7 +24,8 @@ platforms           darwin
 compilers.choose    cc
 mpi.setup
 
-use_configure       no
+# respect MacPorts settings
+patchfiles-append   patch-Makefiles.diff
 
 #Strings used by the variant options
 set HPCm ""
@@ -94,7 +97,6 @@ if {${build_arch} eq "i386" || ${build_arch} eq "x86_64"} {
 #Make sure we are using the correct Makefile for this variant combo
 pre-build {
     build.pre_args      -f Makefile${EXTm}${HPCm}.gcc
-    build.args-append   CC="${configure.cc}"
 }
 
 #We only need the single raxml binary
diff --git a/science/raxml/files/Makefiles.patch b/science/raxml/files/Makefiles.patch
deleted file mode 100644
index 71dff8daada0f..0000000000000
--- a/science/raxml/files/Makefiles.patch
+++ /dev/null
@@ -1,120 +0,0 @@
---- Makefile.MPI.gcc.orig	2011-04-07 06:42:34.000000000 +1000
-+++ Makefile.MPI.gcc	2012-06-21 09:01:59.000000000 +1000
-@@ -3,7 +3,7 @@
- CC = mpicc 
- 
- 
--CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -msse
-+CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -msse  $(EXTRA_CFLAGS)
- 
- 
- LIBRARIES = -lm
-@@ -17,7 +17,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC-MPI : $(objs)
--	$(CC) -o raxmlHPC-MPI $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC-MPI $(objs) $(LIBRARIES) 
- 
- classify.o : classify.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
---- Makefile.PTHREADS.gcc.orig	2011-04-07 06:42:34.000000000 +1000
-+++ Makefile.PTHREADS.gcc	2012-06-21 09:01:51.000000000 +1000
-@@ -4,7 +4,7 @@
- CC = gcc 
- 
- 
--CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse
-+CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse $(EXTRA_CFLAGS)
- 
- 
- LIBRARIES = -lm -pthread
-@@ -18,7 +18,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC-PTHREADS : $(objs)
--	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) 
- 
- classify.o : classify.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
---- Makefile.SSE3.MPI.gcc.orig	2012-06-21 09:01:23.000000000 +1000
-+++ Makefile.SSE3.MPI.gcc	2012-06-21 09:01:34.000000000 +1000
-@@ -2,7 +2,7 @@
- 
- CC = mpicc 
- 
--CFLAGS = -D_WAYNE_MPI -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
-+CFLAGS = -D_WAYNE_MPI -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops $(EXTRA_CFLAGS)
- 
- LIBRARIES = -lm
- 
-@@ -15,7 +15,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC-MPI-SSE3 : $(objs)
--	$(CC) -o raxmlHPC-MPI-SSE3 $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC-MPI-SSE3 $(objs) $(LIBRARIES) 
- 
- classify.o : classify.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
---- Makefile.SSE3.PTHREADS.gcc.orig	2011-04-07 06:42:34.000000000 +1000
-+++ Makefile.SSE3.PTHREADS.gcc	2012-06-21 09:00:59.000000000 +1000
-@@ -3,7 +3,7 @@
- 
- CC = gcc 
- 
--CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
-+CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops $(EXTRA_CFLAGS)  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
- 
- 
- LIBRARIES = -lm -pthread 
-@@ -17,7 +17,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC : $(objs)
--	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) 
- 
- #rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
- classify.o : classify.c $(GLOBAL_DEPS)
---- Makefile.SSE3.gcc.orig	2011-04-07 06:42:34.000000000 +1000
-+++ Makefile.SSE3.gcc	2012-06-21 09:00:41.000000000 +1000
-@@ -3,7 +3,7 @@
- 
- CC = gcc 
- 
--CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops
-+CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops $(EXTRA_CFLAGS)
- 
- LIBRARIES = -lm
- 
-@@ -16,7 +16,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC : $(objs)
--	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) 
- 
- classify.o : classify.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
---- Makefile.gcc.orig	2012-06-21 09:00:26.000000000 +1000
-+++ Makefile.gcc	2012-06-21 09:00:34.000000000 +1000
-@@ -4,7 +4,7 @@
- CC = gcc 
- 
- 
--CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse 
-+CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse $(EXTRA_CFLAGS)
- #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
- 
- LIBRARIES = -lm
-@@ -18,7 +18,7 @@
- GLOBAL_DEPS = axml.h globalVariables.h
- 
- raxmlHPC : $(objs)
--	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
-+	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
- 
- classify.o : classify.c $(GLOBAL_DEPS)
- evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/science/raxml/files/patch-Makefiles.diff b/science/raxml/files/patch-Makefiles.diff
new file mode 100644
index 0000000000000..8f484a24aaeef
--- /dev/null
+++ b/science/raxml/files/patch-Makefiles.diff
@@ -0,0 +1,380 @@
+--- Makefile.AVX.PTHREADS.mac.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.AVX.PTHREADS.mac	2020-05-17 08:10:17.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = clang 
+ 
+-CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+ LIBRARIES = -lm -pthread 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
+ 		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+--- Makefile.AVX.HYBRID.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.AVX.HYBRID.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -2,7 +2,7 @@
+ 
+ CC = mpicc 
+ 
+-CFLAGS = -D_WAYNE_MPI -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX
++CFLAGS += -D_WAYNE_MPI -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX
+ 
+ LIBRARIES = -lm -pthread 
+ 
+@@ -15,7 +15,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC-HYBRID-AVX : $(objs)
+-	$(CC) -o raxmlHPC-HYBRID-AVX $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-HYBRID-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
+ 		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+--- Makefile.SSE3.HYBRID.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.HYBRID.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -2,7 +2,7 @@
+ 
+ CC = mpicc 
+ 
+-CFLAGS = -D_WAYNE_MPI -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
++CFLAGS += -D_WAYNE_MPI -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
+ 
+ LIBRARIES = -lm -pthread
+ 
+@@ -15,7 +15,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC-HYBRID-SSE3 : $(objs)
+-	$(CC) -o raxmlHPC-HYBRID-SSE3 $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-HYBRID-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.AVX.MPI.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.AVX.MPI.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -2,7 +2,7 @@
+ 
+ CC = mpicc 
+ 
+-CFLAGS = -D_WAYNE_MPI -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX
++CFLAGS += -D_WAYNE_MPI -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops -D__AVX
+ 
+ LIBRARIES = -lm
+ 
+@@ -15,7 +15,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC-MPI-AVX : $(objs)
+-	$(CC) -o raxmlHPC-MPI-AVX $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-MPI-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
+ 		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+--- Makefile.SSE3.MPI.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.MPI.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -2,7 +2,7 @@
+ 
+ CC = mpicc 
+ 
+-CFLAGS = -D_WAYNE_MPI -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
++CFLAGS += -D_WAYNE_MPI -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  
+ 
+ LIBRARIES = -lm
+ 
+@@ -15,7 +15,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC-MPI-SSE3 : $(objs)
+-	$(CC) -o raxmlHPC-MPI-SSE3 $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-MPI-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.SSE3.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = gcc 
+ 
+-CFLAGS = -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -16,7 +16,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.HYBRID.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.HYBRID.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -3,7 +3,7 @@
+ CC = mpicc 
+ 
+ 
+-CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse
++CFLAGS += -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops  -D_USE_PTHREADS -msse
+ 
+ 
+ LIBRARIES = -lm -pthread 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC-HYBRID : $(objs)
+-	$(CC) -o raxmlHPC-HYBRID $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-HYBRID $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.SSE3.QuartetMPI.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.QuartetMPI.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = mpicc
+ 
+-CFLAGS = -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops  -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -16,7 +16,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-SSE3-QUARTET-MPI $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-SSE3-QUARTET-MPI $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.AVX.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.AVX.gcc	2020-05-17 08:10:18.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = gcc 
+ 
+-CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -16,7 +16,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
+ 		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+--- Makefile.PTHREADS.mac.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.PTHREADS.mac	2020-05-17 08:10:18.000000000 -0700
+@@ -4,7 +4,7 @@
+ CC = gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops  -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+ LIBRARIES = -lm -pthread
+@@ -18,7 +18,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC-PTHREADS : $(objs)
+-	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.SSE3.PTHREADS.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.PTHREADS.gcc	2020-05-17 08:10:19.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = gcc 
+ 
+-CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+ LIBRARIES = -lm -pthread 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ #rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
+ classify.o : classify.c $(GLOBAL_DEPS)
+--- Makefile.SSE3.PTHREADS.mac.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.PTHREADS.mac	2020-05-17 08:10:19.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = gcc 
+ 
+-CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_USE_PTHREADS -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+ LIBRARIES = -lm -pthread 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ #rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
+ classify.o : classify.c $(GLOBAL_DEPS)
+--- Makefile.AVX.mac.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.AVX.mac	2020-05-17 08:10:19.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = clang
+ 
+-CFLAGS = -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D__SIM_SSE3 -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -16,7 +16,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
+ 		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+--- Makefile.PTHREADS.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.PTHREADS.gcc	2020-05-17 08:10:19.000000000 -0700
+@@ -4,7 +4,7 @@
+ CC = gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops  -D_USE_PTHREADS -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+ LIBRARIES = -lm -pthread
+@@ -18,7 +18,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC-PTHREADS : $(objs)
+-	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-PTHREADS $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.gcc	2020-05-17 08:10:19.000000000 -0700
+@@ -4,7 +4,7 @@
+ CC = gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -msse #-Wall -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.SSE3.mac.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.SSE3.mac	2020-05-17 08:10:19.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = clang
+ 
+-CFLAGS = -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -O2 -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D__SIM_SSE3  -msse3 -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops  #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -16,7 +16,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.MPI.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.MPI.gcc	2020-05-17 08:10:19.000000000 -0700
+@@ -3,7 +3,7 @@
+ CC = mpicc 
+ 
+ 
+-CFLAGS = -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2  -msse
++CFLAGS += -D_WAYNE_MPI -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops  -msse
+ 
+ 
+ LIBRARIES = -lm
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC-MPI : $(objs)
+-	$(CC) -o raxmlHPC-MPI $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-MPI $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
+--- Makefile.AVX.PTHREADS.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.AVX.PTHREADS.gcc	2020-05-17 08:10:19.000000000 -0700
+@@ -3,7 +3,7 @@
+ 
+ CC = gcc 
+ 
+-CFLAGS = -D_USE_PTHREADS  -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_USE_PTHREADS  -D__SIM_SSE3 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+ LIBRARIES = -lm -pthread 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
+ 		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c
+--- Makefile.QuartetMPI.gcc.orig	2013-08-29 06:56:26.000000000 -0700
++++ Makefile.QuartetMPI.gcc	2020-05-17 08:10:19.000000000 -0700
+@@ -4,7 +4,7 @@
+ CC = mpicc
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 -msse -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
++CFLAGS += -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -msse -D_QUARTET_MPI #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ LIBRARIES = -lm
+ 
+@@ -17,7 +17,7 @@
+ GLOBAL_DEPS = axml.h globalVariables.h #mem_alloc.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC-QUARTET-MPI $(objs) $(LIBRARIES) 
++	$(CC) -o raxmlHPC-QUARTET-MPI $(objs) $(LIBRARIES) $(LDFLAGS) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)