--- /dev/null
+###################################################
+#
+# Makefile for mothur
+# Created: June 29, 2010
+#
+###################################################
+
+#
+# Macros
+#
+
+USEMPI ?= no
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES="\"Enter_your_default_path_here\""
+RELEASE_DATE = "\"4/30/2012\""
+VERSION = "\"1.25.0\""
+FORTAN_COMPILER = gfortran
+FORTRAN_FLAGS =
+
+# Optimize to level 3:
+CXXFLAGS += -O3
+
+ifeq ($(strip $(64BIT_VERSION)),yes)
+ #if you are using centos uncomment the following lines
+ #CXX = g++44
+
+ #if you are a mac user use the following line
+ TARGET_ARCH += -arch x86_64
+
+ #if you using cygwin to build Windows the following line
+ #CXX = x86_64-w64-mingw32-g++
+ #CC = x86_64-w64-mingw32-g++
+ #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
+ #TARGET_ARCH += -m64 -static
+
+ #if you are a linux user use the following line
+ #CXXFLAGS += -mtune=native -march=native -m64
+
+ CXXFLAGS += -DBIT_VERSION
+ FORTRAN_FLAGS = -m64
+endif
+
+
+CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
+
+ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
+else
+ CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
+endif
+
+ifeq ($(strip $(CYGWIN_BUILD)),yes)
+ CXXFLAGS += -mno-cygwin
+ LDFLAGS += -mno-cygwin
+endif
+
+# if you do not want to use the readline library, set this to no.
+# make sure you have the library installed
+
+
+ifeq ($(strip $(USEREADLINE)),yes)
+ CXXFLAGS += -DUSE_READLINE
+ LIBS = \
+ -lreadline\
+ -lncurses
+endif
+
+
+ifeq ($(strip $(USEMPI)),yes)
+ CXX = mpic++
+ CXXFLAGS += -DUSE_MPI
+endif
+
+# if you want to enable reading and writing of compressed files, set to yes.
+# The default is no. this may only work on unix-like systems, not for windows.
+
+
+ifeq ($(strip $(USECOMPRESSION)),yes)
+ CXXFLAGS += -DUSE_COMPRESSION
+endif
+
+#
+# INCLUDE directories for mothur
+#
+
+ CXXFLAGS += -I.
+
+#
+# Get the list of all .cpp files, rename to .o files
+#
+
+OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
+
+mothur : fortranSource $(OBJECTS) uchime
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+
+ strip mothur
+
+uchime:
+ cd uchime_src && ./mk && mv uchime .. && cd ..
+
+fortranSource:
+ ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
+
+install : mothur
+# cp mothur ../Release/mothur
+
+%.o : %.c %.h
+ $(COMPILE.c) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.h
+ $(COMPILE.cpp) $(OUTPUT_OPTION) $<
+%.o : %.cpp %.hpp
+ $(COMPILE.cpp) $(OUTPUT_OPTION) $<
+
+
+clean :
+ @rm -f $(OBJECTS)
+ @rm -f uchime
+