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5.2 Other make variables that could be set by the user

SHELL shell used for executing system commands. /bin/sh

CXX c++ compiler. set by OS.

CFLAGS compiler flags. -Wall -ggdb -O2 -pthread

PACKAGENAME the name of the executable file. cold

VERSION the version of the program. 1.0.0

forceremakeconfig indicates whether configuration file needs to be remade.

forceremakevar indicates whether .variable file needs to be remade.

mainsearchdir directory in which application files are based. $(HOME)/$(PACKAGENAME)

prefix directory in which installed files should be stored. /usr/local/

exec_prefix directory in which executable files should be stored. $(prefix)

bindir directory in which the actual binary executable files should be stored.

DESTDIR user input prefix to installation directory.

installbin executable files to be installed. $(PACKAGENAME) DNAml Utilities/setup Utilities/reordermatrix Utilities/summats

installdat data files to be installed. .variables .flags Models/parametermatrices Models/ECMq.txt Data/testtrees Data/testdata Models/mixture Models/models Models/masks Models/standardmodelmatrices Utilities/codonlistexample.txt Utilities/coldcodonorder.txt

installdoc documentation files to be installed. Documentation/ Documentation/ Documentation/ Documentation/

INSTALL command for installing programs. set by OS.