|Installing PHYLIP 3.6|
Let's assume that you have fetched the appropriate executables archives (if any) for your machine, together with the Documentation and Sources archive.
These archives are not simply a single executable for general use. Instead they are a (large) number of files, squished together into one file, and thus called an "archive". You have to go through a step which involves getting all the files out of the archive and into a folder on your machine.
We will give these instructions for four different kinds of systems, Windows, Mac OS X, Linux or Unix systems, and Mac OS 8 or 9. Then we will describe how to access the documentation after installing the package.
When you click to download the Zip archive, most recent Windows systems will open a window which asks whether you want to open the archive with Windows Explorer, or want to Save the archive. Choose to Save it. It will be placed in the Downloads folder of your account. There are now two possibilities:
It will create a folder called Phylip-3.695. So if you place the archive on the Desktop, it will make that folder there.
After the extraction is done, you will find the phylip-3.695 folder which has three folders within it, called doc, exe, and src. There is also a web page phylip.html. You should read this in your browser. It contains links to the main documentation web page main.html and to the other documentation pages and programs.
Note: There has been a report that on Windows Vista (specifically the report was for Service Pack 2 on Home Edition) that if you extract the files into a folder that is somewhere under Program Files, they may not work properly. You can avoid this problem if you extract them into a folder which is somewhere in your own folders.
What to do if the Avast virus-checking software complains: We have had several reports that the Avast virus-checking software will not allow PHYLIP 3.695 to be installed because it concludes that it contains a virus. It is complaining about our Java front end for program Drawgram (a file called DrawGramJava.exe). We have had this file checked carefully by our virus-checking company, Sophos, and they find no virus there. There is the invocation of a "shell" in that Java code that may alarm Avast, which is being overcautious. If you can extract and install the code on someone else's machine, one which has differemt virus-checking software, you then may be able to copy the folder over to your machine.
|Macintosh Mac OS X|
The archives for Intel iMac and PowerMac Mac OS X are in the Apple .dmg disk image format. There is one .dmg disk image distributed. It is 12 Megabytes in size, and is compressed; when uncompressed it is several times larger.
It contains what looks like a normal folder called phylip-3.695, but you should not use the programs while they are in that folder. It is important that you use a copy of the contents of the disk image elsewhere on your system. Decide where the folder phylip-3.695 is going to reside, and copy that folder to that new location. Within it is all the source code, documentation, and executables.
The executables are 32-bit "universal binaries" that will run on either the Intel iMacs or the older G3's, G4's or G5's that have PowerMac processors. (Basically the universal binaries are each simply a pair of executables set up so that the processor chooses the right one and runs it).
Enabling the programs to be run in a Terminal windows by typing their names: A set of links can be set up in the exe folder to enable you to run the programs by simply typing their name. If these are absent, which they should not be, there is one additional set of steps you need to do:
This setting up of these links needs to done only once, and they will be available thereafter.
Fixing the Mountain Lion permission problem: The latest Mac OS X operating system version, Mountain Lion, will not run executables of PHYLIP programs when you click in their icons. It complains that the developer name is unknown. This is a security feature. There is an easy workaround for this that needs to be done once for each program. If this occurs, try control-clicking on the program icon instead. Select Open. When you are then asked whether you want to open this program, select Open. The program will open. It also allows the program to be opened in the future by clicking on the executable icon. So it only needs to be done once for each of the programs in PHYLIP, and after that the program can be run by clicking on the icon for that program. We hope to avoid this in future versions by signing the programs with my Apple Developer identity. As far as I know, this problem does not arise if you open a program in a Terminal window by typing its name.
|Linux and Unix|
You can easily install PHYLIP and compile it yourself on a Linux or Unix system, provided that you have a C compiler on your system. (On some Linux systems and in some recent versions of Mac OS X the C compiler is not installed by default, and you may have to make sure that it is installed).
The archive for Linux or Unix systems is just the Documentation and Sources archive.
You can extract the files from the archive by putting it into a folder
by itself, getting into that folder, and giving the command
tar -zxvf phylip-3.696.tar.gz
To make executables, use your C compiler. It is probably as simple as
going into the src directory, copying Makefile.unx and
calling the copy Makefile, and then typing the command
make installwhich will cause the programs to be compiled and the executables and font files installed in the exe directory. Alternatively, you can type the command
make -f Makefile.unx installinstead.
If there are problems with the compilation, read the relevant sections of main.html and also the beginning of the Makefile.
With luck this will work. After the compilation the executables and their font files will be in folder exe.
|Macintosh Mac OS 8 or Mac OS 9|
We don't think there are many Mac OS 8 or Mac OS 9 machines around any more -- Apple long ago abandoned that operating system, and it is probably not safe to use it on the Internet as it has not been upgraded to cope with recent security threats. We no longer distribute Mac OS 8 or 9 executables for our most recent versions of PHYLIP. Nevertheless, we do make available a Stuffit (.sit) archive of executables for PHYLIP 3.65, just in case anyone needs it.
The archives for Mac OS 8, Mac OS 9 Macintoshes are self-extracting archives. If you are fetching the files using a Web browser directly from your Mac, it will probably automatically invoke Stuffit Expander to unpack the archives into self-extracting archives. Self-extracting archives are archives with a small self-extraction program on their front, so that when they are run as programs they write a great many files into a folder.
Our default distribution is of a single large (4.9 Megabyte) Stuffit archive called phylip3.65.sit. This should automatically be unstuffed as it is downloaded. It contains the source code, documentation, and Mac OS executables.
However, at the moment we have reports of trouble running the unstuffed archives. Recent versions of Mac OS 9, and also the Classic environment under Mac OS X, seem to regard the executables files as text files, and they try to open them under SimpleText, which of course does not work.
Some people may wish instead to download these as a series of four archives. This might be necessary, for example, if you wanted to transfer them to a machine that was not connected to the Internet, and needed them each to be small enough to write onto a floppy disk.
If you choose to download these instead of the single Stuffit archive,
and our system does automatically invoke Stuffit Expander, four self
extracting archives will
be created on your desktop, and their file names will end in
If you have Stuffit Expander, you can use it to expand them.
Once the archives are downloaded and extracted, they will put folders on the desktop. One is called phylip and contains folders doc and src as well as a web page phylip.html. There are 307 files in all, as these include the documentation files, source code files, and compilation support files. You may have to be patient while the archive is being extracted.
The three archives of Macintosh Mac OS 8 and Mac OS 9 executables will create folders exe, exe.1, exe.2 and exe.3 on the desktop when they are extracted. For some reason we could not create these inside the phylip folder, but that is where these files need to be put. Do the following:
|Reading the documentation|
The main folder contains a web page, phylip.html. You should start by reading it (either by clicking on it to activate your browser, or calling it to the attention of your browser in some other way such as drag-and-drop). It contains links to the documentation web pages, including the main documention page main.html, which you should read.
|Executables available from others|
Executables packages are also available from others. For the moment, these are for earlier versions of PHYLIP (such as 3.61 and 3.68). They include executables for Red Hat Linux, Debian Linux, NetBSD Unix for Intel-compatible processors, and FreeBSD Unix. For links see our downloads page.
... to the PHYLIP home page