Makefile.unix

#
# Generic Linux/Unix Makefile for PHYLIP 4.0.
#
# You should not need to change anything, though if you want you could
# change the first (noncomment) statement -- the one that sets the
# folder (directory) in which the executables will be placed -- to some
# directory location that might be more useful.
#
# The compressed tar archive phylip.tar.Z when uncompressed and extracted
# puts the source code into a directory ./src, and also makes two other
# directories ./exe and ./doc for the final executables and the documentation
# files.  Only change the EXEDIR settings if you want something different
# from that structure.
#
# If it causes trouble in compiling, the CFLAGS statement below may also need
# to be changed.
#
# To use the PHYLIP v4.0 Makefile, type one of these:
#
#      make install         to compile the whole package and install
#                           the executables in $(EXEDIR), and then
#                           remove the object files to save space.
#
#      make all             to compile the whole package but not install it
#                           or remove the object files.
#
#      make put             to move the executables into $(EXEDIR).
#
#      make clean           to remove all object files and executables from the
#                           current directory.
#
#      make dnaml           to compile and link one program, (in this example,
#                           Dnaml) and leave the executable and object files
#                           in the current directory (where the source code is).
#                           You will have to move the executable in to the
#                           executables directory (e.g. "mv dnaml ../exe")
#                           Note that the program name should be lower case.
#
# ----------------------------------------------------------------------------
# Starting here is the section where you may want to change things.
# ----------------------------------------------------------------------------
#
# These are the statements we have been talking about:
#
# One of the reasons for changing them would be to put the executables
# on a different file system.  The default configuration is to have within
# the overall PHYLIP directory three subdirectories:
#   "src" for source code, "exe" for the executables, and
#   "doc" for the documentation files.
#
# The following specifies the directory where the executables will be placed:
EXEDIR = ../exe
#
# The following fetches the name of the Unix or Linux shell
#
UNAME := $(shell uname)
#
# ----------------------------------------------------------------------------
#
# The following statements set these variables:
#
#    CFLAGS -- compiler directives needed to compile most programs
#    DFLAGS -- compiler directives needed to compile draw programs
#    LIBS   -- non-default system libraries needed to compile most programs
#    DLIBS  -- non-default system libraries needed to compile draw programs
#    CC     -- the name (and, optionally, location) of your C compiler
#    DC     -- the name (and, optionally, location) of your C compiler
#               for draw programs
#
# We've provided a set of possible values for each variable.
#
# The value used is the one without a "#" at the beginning of the line.
#
# To try an alternate value, make sure the one you want has no "#"
# as its first character and that all other possibilities have "#" for
# their first character.
#
# Advanced users may need to further edit one of the alternatives in
# order to correctly compile on their system.
#
# ----------------------------------------------------------------------------
#
# In the following statements (the ones that set CFLAGS, DFLAGS, LIBS
# and DLIBS, CC and DC) you should make sure each is set properly.
# Usually this will simply involve making sure that the proper statement
# has no "#" as its first character and that all other possibilities
# have "#" for their first character.
#
# ----------------------------------------------------------------------------
#
# This is the CFLAGS statement:
#
# If these statements say "-g"  and that causes trouble, remove the "-g".
# If the "-lX11" does not work (X compiling not working), you may want to
# remove that switch or fix it.
#
# Here are some possible CFLAGS statements:
#
# A minimal one:
#CFLAGS  = -g
CFLAGS = -Wl -zmuldefs
#
# A basic one for debugging:
#CFLAGS  = -g -Wall
#
# For MacOS using the clang compiler
#CFLAGS = -g
#
# For some serious debugging using GNU GCC.  This raises debug warning
#  reporting to highest level possible.
#ifeq ($(MODE), GDB)
#   No optimization; intended for debugging with GDB.  Debug level
#    is "-ggdb3", maximal for GDB.  Originally was "-g".  Maximal debug
#    information preserved (at cost of "-Wuninitialized" warning).
#CFLAGS=-ggdb3 -std=c99 -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes -Wunused -Wextra -pedantic -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
#else
#   Minimal optimization; intended for debugging via compilation but not
#   using GDB. Debug level is "-g", good for debugging but not maximal for GDB.
#CFLAGS=-g -std=c99 -O -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes -Wunused -Wextra -pedantic -Wuninitialized -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
#  In case value is not defined (or bogus), give MODE a value to indicate
#   "NORMAL" compilation; used only for display.
#MODE=NORMAL
#endif
#
# An optimized one for gcc:
#CFLAGS  = -O3 -fomit-frame-pointer
#
# For some serious debugging using Gnu gcc:
CFLAGS=-g -Wall -Wmain -Wmissing-prototypes -Wreturn-type -Wstrict-prototypes -Wunused -Werror -Wredundant-decls -Waggregate-return -Wcast-align -Wcomment
#
# These are for specific systems, in these cases fairly obsolete ones:
#
# For Digital Alpha systems with Compaq Tru64 Unix
# (however, be aware that this may cause floating-point problems in programs
#  like Dnaml owing to not using IEEE floating point standards):
#CFLAGS = -fast
#
# Optimized one for the IBM Visualage compiler for Linux or AIX on IBM pSeries
#CFLAGS = -O -qmaxmem=-1 -qarch=auto -qtune=auto
#
# ----------------------------------------------------------------------------
#
# This is the DFLAGS statement.  It specifies compiler behavior for the
# programs drawgram and drawtree.  It adds additional information to
# the $(CFLAGS) value so these programs can use X11 graphics.
#
# A minimal one -- drawing programs will run, but will not use X11 graphics.
# If you use this one, you must also use the minimal value for $(DLIBS).
#DFLAGS  = -DX $(CFLAGS)
#
# A basic one for debugging:
#DFLAGS  = -g -DX
#
# For Gnu C++ for runs:
#DFLAGS  = -I/usr/X11R6/include -O3 -DX -fomit-frame-pointer
#
# For Linux with X Windows development packages installed
# or for MacOS X with X Windows installed:
DFLAGS = -DX $(CFLAGS) -I/usr/X11R6/include
#
# For Digital Alpha systems with Compaq Tru64 Unix:
#DFLAGS = -DX -fast
#
# For IBM Visualage compiler on Linux or AIX for the IBM pSeries
#DFLAGS  = -DX $(CFLAGS)
#
# ----------------------------------------------------------------------------
#
# These are the libraries for the CC and DC compiles, respectively:
#
# Use this one to include debugging facility.
#LIBS    = Slist.o phylip.o debug.o
#
LIBS    = Slist.o phylip.o
LDADD   = -lm
#
# If the Xlib library for the X windowing system is somewhere
# unexpected, you may have to change the path /usr/X11R6/lib in this one.
#
# For gcc for Linux with X windows development packages installed
#  or for MacOS X with X windows installed
#  or for IBM pSeries with Linux:
DLIBS= -L/usr/X11R6/lib/ -lX11 -lXt
# was: DLIBS= -L/usr/X11R6/lib/ -lX11 -lXaw -lXt   Athena widgets available? needed?
#
# For IBM Visualage compiler for AIX:
#DLIBS= -L/usr/X11R6/lib/ -lX11 -lXaw -lXt -lXmu -lXext
#
# ----------------------------------------------------------------------------
#
# The next two assignments are the invocations of the compiler for the
# ordinary compiles and the tree-drawing programs, CC and DC:
#
# This one specifies the "cc" C compiler:
#CC        = cc $(CFLAGS)
#
#  To use GCC instead, if it is not the compiler that "cc" invokes:
CC         = gcc $(CFLAGS)
#
# For the clang compiler on MacOS
#CC         = clang $(CFLAGS)
#
# For IBM compiler for Linux or AIX on IBM pSeries
#CC        = xlc $(CFLAGS)
#
# This one specifies the "cc" C compiler for the Draw programs:
#DC        = cc $(DFLAGS)
#
# To use GCC for the Draw programs instead, if it is not the compiler that "cc" invokes:
DC         = gcc $(DFLAGS)
#
# For IBM compiler for the Draw programs for Linux or AIX on IBM pSeries:
#DC        = xlc $(DFLAGS)
#
# ----------------------------------------------------------------------------
# After this point there should not be any reason to change anything.
# ----------------------------------------------------------------------------
#
# The list of programs.
# Draw programs are listed last since they are the most likely to cause
# compilation or linking problems.
#
PROGS = clique codml consense contml contrast dnacomp dnadist dnainvar dnaml \
        dnamlk dnamove dnapars dnapenny dolmove dollop dolpenny factor fitch \
        gendist kitsch mix move neighbor pars penny proml promlk protdist protpars \
        restdist restml retree seqboot threshml treedist drawgram drawtree

DYLIBS := libclique.so libconsense.so libcontml.so libdnacomp.so libdnadist.so libdnainvar.so
DYLIBS += lidnaml.so libdnapars.so libdnapenny.so libdollop.so libdolpenny.so libdrawgram.so
DYLIBS += libdrawtree.so libfactor.so libfitch.so libgendist.so libmix.so libneighbor.so libpars.so 
DYLIBS += libpenny.so libprotpars.so libproml.so libprotdist.so librestdist.so libseqboot.so
DYLIBS += libtreedist.so

SHARED := -shared

# These for now, until we get this stuff debugged.
BUILD_FAILURES := codml contml dnamlk dnamove fitch kitsch neighbor pars proml promlk protpars restml retree
PROGS := $(filter-out $(BUILD_FAILURES),$(PROGS))
DYLIBS :=

ifeq ($(UNAME),Darwin)
  SHARED :=
else ifeq ($(UNAME),Linux)
  DFLAGS := -DX $(CFLAGS)
  DLIBS :=
else
  $(error Only know how to build for OS/X and Linux, not $(UNAME))
endif


#
# General commands.
#

# These targets do not produce a file of their namesake, so tell make not
# to bother looking:
.PHONY: help all introduce put clean install

#
#  The first target is executed if you just type "make".  It tells you how to use the Makefile.
#
help:
	@echo ""
	@echo " To use the PHYLIP v4.0 Makefile, type:"
	@echo ""
	@echo "     make install           to compile the whole package and install"
	@echo "                            the executables in $(EXEDIR), and then"
	@echo "                            remove the object files to save space."
	@echo ""
	@echo "     make all               to compile the whole package but not install it"
	@echo "                            or remove the object files."
	@echo ""
	@echo "     make put               to move the executables into $(EXEDIR)."
	@echo ""
	@echo "     make clean             to remove all object files and executables from the"
	@echo "                            current directory."
	@echo ""
	@echo "     make dnaml             to compile and link one program, (in this example,"
	@echo "                            Dnaml) and leave the executable and object files"
	@echo "                            in the current directory (where the source code is)."
	@echo ""
	@echo "                            You will have to move the executable into the"
	@echo "                            executables directory (e.g. "mv dnaml $(EXEDIR)")"
	@echo "                            Note that the program name should be lower case."

all:    introduce $(PROGS) $(DYLIBS)
	@echo ""
	@echo "Successfully built programs:"
	@printf "\t$(PROGS)\n"
	@echo ""
	@echo "Did not try to build programs:"
	@printf "\t$(BUILD_FAILURES)\n"

introduce:
	@echo ""
	@echo "Building PHYLIP version 4.0."

install: pre-clean all put clean
	@echo ""
	@echo "Done."

put:
	@echo ""
	@echo "Installing PHYLIP v4.0 binaries in $(EXEDIR)."
	@mkdir -p $(EXEDIR)
	@mv $(PROGS) $(EXEDIR)
	@echo ""
	@echo "Installing Hershey font files in $(EXEDIR)."
	@cp font* $(EXEDIR)
	@echo ""
	@echo "Finished installation."

pre-clean:
	@echo ""
	@echo "Removing preexisting executables."
	@rm -rf $(EXEDIR)/*
	@echo ""
	@echo "Ready for new executables."

clean:
	@echo ""
	@echo "Removing object files to save space."
	@rm -f *.o
	@echo ""
	@echo "Finished removing object files.  Now will remove"
	@echo "executable files from the current directory, but not from the"
	@echo "executables directory.  (If some are not here, the makefile"
	@echo "may terminate with an error message but this is not a problem.)"
	@echo ""
	@echo "Removing executables from this directory."
	@rm -f $(PROGS)
	@echo ""
	@echo "Finished cleanup."

#
# Compile the shared stuff.
#

Slist.o:      Slist.c Slist.h
	$(CC) -c Slist.c $(SHARED) -fPIC

phylip.o:     phylip.c Slist.h
	$(CC) -c phylip.c $(SHARED) -fPIC 

# Add this to include debugging facility.
# debug.o:      debug.c debug.h phylip.h Slist.h
#	$(CC) -c debug.c

seq.o:        ml.c bl.c seq.c phylip.h seq.h
	$(CC) -c seq.c $(SHARED) -fPIC

bl.o:         phylip.h bl.h
	$(CC) -c bl.c $(SHARED) -fPIC 

ml.o:         bl.c ml.c phylip.h bl.h ml.h
	$(CC) -c ml.c $(SHARED) -fPIC 

mldna.o:         mldna.h phylip.h bl.h ml.h bl.c ml.c mldna.c 
	$(CC) -c mldna.c $(SHARED) -fPIC 

rest_common.o:  rest_common.c rest_common.h phylip.h
	$(CC) -c rest_common.c $(SHARED) -fPIC

prom_common.o:  prom_common.c prom_common.h phylip.h
	$(CC) -c prom_common.c $(SHARED) -fPIC

parsimony.o:  parsimony.c phylip.h parsimony.h
	$(CC) -c parsimony.c $(SHARED) -fPIC

dnaparsimony.o:  dnaparsimony.c phylip.h parsimony.h dnaparsimony.h
	$(CC) -c dnaparsimony.c $(SHARED) -fPIC

disc.o:       disc.c phylip.h disc.h
	$(CC) -c disc.c $(SHARED) -fPIC

discreteparsimony.o:   discreteparsimony.c discreteparsimony.h phylip.h parsimony.h
	$(CC) -c discreteparsimony.c $(SHARED) -fPIC

dollo.o:      dollo.c phylip.h dollo.h
	$(CC) -c dollo.c $(SHARED) -fPIC

wagner.o:     wagner.c phylip.h wagner.h
	$(CC) -c wagner.c $(SHARED) -fPIC

dist.o:       dist.c phylip.h dist.h ml.h
	$(CC) -c dist.c $(SHARED) -fPIC

cont.o:       cont.c cont.h phylip.h
	$(CC) -c cont.c $(SHARED) -fPIC

moves.o:      moves.c phylip.h moves.h
	$(CC) -c moves.c

cons.o:       cons.c cons.h phylip.h
	$(CC) -c cons.c $(SHARED) -fPIC

pmatrix.o:    pmatrix.c pmatrix.h
	$(CC) -c pmatrix.c $(SHARED) -fPIC

matrixd.o:    matrixd.c matrixd.h
	$(CC) -c matrixd.c $(SHARED) -fPIC

drawinit.o:   drawinit.c draw.c draw2.c draw.h
	$(CC) -c drawinit.c $(SHARED) -fPIC

#
# Compile the individual programs.
#

clique.o:     clique.c disc.h phylip.h
	$(CC) -c clique.c $(SHARED) -fPIC

codml.o:      codml.c ml.h bl.h seq.h phylip.h
	$(CC) -c codml.c $(SHARED) -fPIC

consense.o:   consense.c cons.h phylip.h
	$(CC) -c consense.c $(SHARED) -fPIC

contml.o:     contml.c cont.h phylip.h bl.h ml.h Slist.h
	$(CC) -c contml.c $(SHARED) -fPIC

contrast.o:   contrast.c cont.h phylip.h bl.h ml.h
	$(CC) -c contrast.c $(SHARED) -fPIC

dnacomp.o:    dnacomp.c seq.h phylip.h dnaparsimony.h parsimony.h
	$(CC) -c dnacomp.c $(SHARED) -fPIC

dnadist.o:    dnadist.c seq.h pmatrix.h phylip.h
	$(CC) -c dnadist.c $(SHARED) -fPIC

dnainvar.o:   dnainvar.c seq.h phylip.h
	$(CC) -c dnainvar.c $(SHARED) -fPIC

dnaml.o:      dnaml.c seq.h bl.h ml.h mldna.h phylip.h
	$(CC) -c dnaml.c $(SHARED) -fPIC

dnamlk.o:     dnamlk.c seq.h bl.h ml.h phylip.h
	$(CC) -c dnamlk.c $(SHARED) -fPIC

dnamove.o:    dnamove.c seq.h moves.h phylip.h parsimony.h dnaparsimony.h
	$(CC) -c dnamove.c

dnapars.o:    dnapars.c seq.h phylip.h parsimony.h dnaparsimony.h
	$(CC) -c dnapars.c $(SHARED) -fPIC

dnapenny.o:   dnapenny.c seq.h phylip.h parsimony.h dnaparsimony.h
	$(CC) -c dnapenny.c $(SHARED) -fPIC

dolmove.o:    dolmove.c disc.h moves.h dollo.h phylip.h
	$(CC) -c dolmove.c

dollop.o:     dollop.c disc.h dollo.h phylip.h
	$(CC) -c dollop.c $(SHARED) -fPIC

dolpenny.o:   dolpenny.c disc.h dollo.h phylip.h
	$(CC) -c dolpenny.c $(SHARED) -fPIC

draw.o:       draw.c draw.h phylip.h
	$(DC) -c draw.c $(SHARED) -fPIC

draw2.o:      draw2.c draw.h phylip.h
	$(DC) -c draw2.c $(SHARED) -fPIC

drawgram.o:   drawinit.c drawgram.c draw.h phylip.h Slist.h
	$(DC) -c drawgram.c $(SHARED) -fPIC

drawtree.o:   drawinit.c drawtree.c draw.h phylip.h Slist.h
	$(DC) -c drawtree.c $(SHARED) -fPIC

factor.o:     factor.c phylip.h
	$(CC) -c factor.c $(SHARED) -fPIC

fitch.o:      fitch.c dist.h phylip.h bl.h ml.h Slist.h
	$(CC) -c fitch.c $(SHARED) -fPIC

gendist.o:    gendist.c phylip.h pmatrix.c pmatrix.h
	$(CC) -c gendist.c $(SHARED) -fPIC

interface.o:  interface.c interface.h draw.h phylip.h
	$(DC) -c interface.c $(SHARED) -fPIC

kitsch.o:     kitsch.c dist.h bl.h ml.h phylip.h
	$(CC) -c kitsch.c $(SHARED) -fPIC

mix.o:        mix.c disc.h wagner.h phylip.h
	$(CC) -c mix.c $(SHARED) -fPIC

move.o:       move.c disc.h moves.h wagner.h phylip.h
	$(CC) -c move.c

neighbor.o:   neighbor.c dist.h phylip.h
	$(CC) -c neighbor.c $(SHARED) -fPIC

pars.o:       pars.c discreteparsimony.h phylip.h parsimony.h
	$(CC) -c pars.c $(SHARED) -fPIC

penny.o:      penny.c disc.h wagner.h phylip.h
	$(CC) -c penny.c $(SHARED) -fPIC

proml.o:      proml.c seq.h bl.h ml.h phylip.h prom_common.h prom_common.c
	$(CC) -c proml.c $(SHARED) -fPIC

promlk.o:     promlk.c seq.h bl.h ml.h phylip.h prom_common.h prom_common.c
	$(CC) -c promlk.c $(SHARED) -fPIC

protdist.o:   protdist.c seq.h phylip.h pmatrix.c pmatrix.h
	$(CC) -c protdist.c $(SHARED) -fPIC

protpars.o:   protpars.c seq.h phylip.h parsimony.h
	$(CC) -c protpars.c $(SHARED) -fPIC

restdist.o:   restdist.c rest_common.h seq.h phylip.h pmatrix.c pmatrix.h
	$(CC) -c restdist.c $(SHARED) -fPIC

restml.o:     restml.c rest_common.h seq.h bl.h ml.h phylip.h
	$(CC) -c restml.c $(SHARED) -fPIC

retree.o:     retree.c moves.h phylip.h
	$(CC) -c retree.c

seqboot.o:    seqboot.c phylip.h
	$(CC) -c seqboot.c $(SHARED) -fPIC

threshml.o:   threshml.c cont.h phylip.h Slist.h
	$(CC) -c threshml.c $(SHARED) -fPIC

treedist.o:   treedist.c cons.h phylip.h
	$(CC) -c treedist.c $(SHARED) -fPIC

#
# Link the individual programs.
#

clique:       clique.o disc.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

codml:        codml.o bl.o ml.o seq.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

consense:     consense.o cons.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

contml:       contml.o cont.o ml.o bl.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

contrast:     contrast.o cont.o ml.o bl.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnacomp:      dnacomp.o seq.o parsimony.o dnaparsimony.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnadist:      dnadist.o pmatrix.o matrixd.o seq.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnainvar:     dnainvar.o seq.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnaml:        dnaml.o seq.o bl.o ml.o mldna.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnamlk:       dnamlk.o seq.o bl.o ml.o mldna.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnamove:      dnamove.o seq.o moves.o parsimony.o dnaparsimony.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnapars:      dnapars.o seq.o parsimony.o dnaparsimony.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dnapenny:     dnapenny.o seq.o parsimony.o dnaparsimony.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dolmove:      dolmove.o disc.o moves.o dollo.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dollop:       dollop.o disc.o dollo.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

dolpenny:     dolpenny.o disc.o dollo.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

drawgram:     drawgram.o draw.o draw2.o drawinit.o $(LIBS)
	$(DC) $(DLIBS) $^ $(LDADD) -o $@

drawtree:     drawtree.o draw.o draw2.o drawinit.o $(LIBS)
	$(DC) $(DLIBS) $^ $(LDADD) -o $@

factor:       factor.o disc.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

fitch:        fitch.o dist.o bl.o ml.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

gendist:      gendist.o pmatrix.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

kitsch:       kitsch.o dist.o bl.o ml.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

mix:          mix.o disc.o wagner.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

move:         move.o disc.o moves.o wagner.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

neighbor:     neighbor.o dist.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

pars:         pars.o discreteparsimony.o parsimony.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

penny:        penny.o disc.o wagner.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

proml:        proml.o prom_common.o seq.o bl.o ml.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

promlk:       promlk.o prom_common.o seq.o bl.o ml.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

protdist:     protdist.o seq.o pmatrix.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

protpars:     protpars.o seq.o parsimony.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

restdist:     restdist.o rest_common.o seq.o pmatrix.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

restml:       restml.o rest_common.o seq.o bl.o ml.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

retree:       retree.o moves.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

seqboot:      seqboot.o seq.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

threshml:     threshml.o cont.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@

treedist:     treedist.o cons.o $(LIBS)
	$(CC) $^ $(LDADD) -o $@


# Dynamic libraries (.so)

libclique.so:   clique.o disc.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libclique.so $(SHARED) -fPIC clique.c disc.c phylip.c

libcodml.so:    codml.o ml.o bl.o seq.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libcodml.o $(SHARED) -fPIC codml.c ml.c bl.c seq.c phylip.c Slist.c

libconsense.so:	consense.o cons.o phylip.o Slist.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libconsense.so $(SHARED) -fPIC consense.c cons.c phylip.c Slist.c

libcontml.so:   contml.o cont.o ml.o bl.o phylip.o phylip.h ml.h Slist.h $(LIBS)
	$(CC) $(CFLAGS) -o libcontml.so $(SHARED) -fPIC contml.c cont.c ml.c bl.c phylip.c Slist.c

libdnacomp.so: dnacomp.o seq.o parsimony.o dnaparsimony.o phylip.o $(LIBS)
	$(CC) $(CFLAGS) -o libdnacomp.so $(SHARED) -fPIC dnacomp.c seq.c dnaparsimony.c parsimony.c phylip.c Slist.c

libdnadist.so:	dnadist.o pmatrix.o seq.o phylip.o phylip.h seq.h  $(LIBS)
	$(CC) $(CFLAGS) -o libdnadist.so $(SHARED) -fPIC dnadist.c seq.c phylip.c pmatrix.c matrixd.c Slist.c

libdnainvar.so: dnainvar.o seq.o phylip.o $(LIBS)
	$(CC) $(CFLAGS) -o libdnainvar.so $(SHARED) -fPIC dnainvar.c seq.c phylip.c Slist.c

libdnaml.so:	dnaml.o seq.o ml.o bl.o $(LIBS)
	$(CC) $(CFLAGS) -o libdnaml.so $(SHARED) -fPIC dnaml.c seq.c ml.c bl.c phylip.c Slist.c -shared -fPIC

libdnapars.so: dnapars.o seq.o parsimony.o dnaparsimony.o phylip.o $(LIBS)
	$(CC) $(CFLAGS) -o libdnapars.so $(SHARED) -fPIC dnapars.c seq.c dnaparsimony.c parsimony.c phylip.c Slist.c

libdnapenny.so: dnapenny.o seq.o phylip.o $(LIBS)
	$(CC) $(CFLAGS) -o libdnapenny.so $(SHARED) -fPIC dnapenny.c seq.c phylip.c Slist.c

libdollop.so:    dollop.o disc.o dollo.o wagner.o dollo.h phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libdollop.so $(SHARED) -fPIC dollop.c dollo.c disc.c wagner.c phylip.c Slist.c

libdolpenny.so:    dolpenny.o disc.o wagner.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libdolpenny.so $(SHARED) -fPIC dolpenny.c disc.c wagner.c phylip.c Slist.c

libdrawgram.so:   drawgram.o draw.o draw2.o drawinit.o $(LIBS)
	$(CC) $(CFLAGS) -o libdrawgram.so $(SHARED) -fPIC drawgram.c draw.c draw2.c drawinit.c Slist.c phylip.c

libdrawtree.so:   drawtree.o draw.o draw2.o drawinit.o $(LIBS)
	$(CC) $(CFLAGS) -o libdrawtree.so $(SHARED) -fPIC drawtree.c draw.c draw2.c drawinit.c Slist.c phylip.c

libfactor.so:   factor.o phylip.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libfactor.so $(SHARED) -fPIC factor.c phylip.c

libfitch.so:	fitch.o phylip.o dist.o bl.o ml.o $(LIBS)
	$(CC) $(CFLAGS) -o libfitch.so $(SHARED) -fPIC fitch.c phylip.c bl.c ml.c dist.c Slist.c

libgendist.so:  gendist.o phylip.o pmatrix.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libgendist.so $(SHARED) -fPIC gendist.c pmatrix.c phylip.c Slist.c

libmix.so:    mix.o disc.o wagner.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libmix.so $(SHARED) -fPIC mix.c disc.c wagner.c phylip.c Slist.c

libneighbor.so: neighbor.o dist.o phylip.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libneighbor.so $(SHARED) -fPIC neighbor.c dist.c phylip.c Slist.c

libpars.so: pars.o parsimony.o discreteparsimony.o phylip.o $(LIBS)
	$(CC) $(CFLAGS) -o libpars.so $(SHARED) -fPIC pars.c discreteparsimony.c parsimony.c phylip.c Slist.c

libpenny.so:    penny.o disc.o wagner.o phylip.h $(LIBS)
	$(CC) $(CFLAGS) -o libpenny.so $(SHARED) -fPIC penny.c disc.c wagner.c phylip.c Slist.c

libproml.so:	proml.o seq.o ml.o bl.o ml.c prom_common.c $(LIBS)
	$(CC) $(CFLAGS) -o libproml.so $(SHARED) -fPIC proml.c prom_common.c seq.c ml.c bl.c phylip.c Slist.c -shared -fPIC

libprotdist.so:  protdist.o pmatrix.o seq.o $(LIBS)
	$(CC) $(CFLAGS) -o libprotdist.so $(SHARED) -fPIC protdist.c seq.c pmatrix.c phylip.c Slist.c

libprotpars.so: protpars.o seq.o parsimony.o dnaparsimony.o phylip.o $(LIBS)
	$(CC) $(CFLAGS) -o libprotpars.so $(SHARED) -fPIC protpars.c seq.c dnaparsimony.c parsimony.c phylip.c Slist.c

librestdist.so:  restdist.o rest_common.o seq.o pmatrix.o $(LIBS)
	$(CC) $(CFLAGS) -o librestdist.so $(SHARED) -fPIC restdist.c rest_common.c seq.c pmatrix.c phylip.c Slist.c

libseqboot.so:  seqboot.o seq.o $(LIBS)
	$(CC) $(CFLAGS) -o libseqboot.so $(SHARED) -fPIC seqboot.c seq.c phylip.c Slist.c

libtreedist.so: treedist.o cons.o $(LIBS)
	$(CC) $(CFLAGS) -o libtreedist.so $(SHARED) -fPIC treedist.c cons.c phylip.c Slist.c

# End.