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, MacOS, Linux or Unix systems, 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:

  1. If it has been extracted, a folder called phylip-3.698 (one which does not have the image of a zipper on the folder icon) will also be there. Move that folder to where you want it to be. Do not try to use the programs or documentation while it is still in the Downloads folder.

  2. If it has not been extracted, there will be a Zip archive folder (one which has a zipper on the folder icon). Move it to where you want it to be. This Zip archive can then be extracted by right-clicking on its icon and selecting Extract All from the menu that appears.

    It will create a folder called Phylip-3.698. 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-3.698 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, which you can usually do by clicking on the file. 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.

Issue with Drawgram or Drawtree not finding .dll libraries. There has been a report that using Drawgram or Drawtree's Java front-end failed because a Dynamic Link Library (.dll file) is not found. This has happened when people have a 64-bit Windows system but install the 32-bit version of PHYLIP. There are now both 64- and 32-bit versions of the executables available. If the problem with finding DLL files persists in spite of you having the correct version of the Windows executables, try installing the latest version of Java. (Thanks to Isha Androiya).


Apple Mac OS

The archives for Intel iMac 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 that folder is in the Downloads 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 move that folder to that new location. Within it is all the source code, documentation, and executables.

The executables are 64-bit binaries which will run on Intel iMacs produced since about 2010.

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:

  1. Open a Terminal window (which you will find in the Utilities folder of the Applications folder).
  2. At the prompt, change to the folder where the PHYLIP executables are kept. For example, if you have folder phylip-3.695 on your desktop, type in the command
    cd ~/Desktop/phylip-3.695/
  3. Copy the file linkmac from the src folder to this exe folder (by giving the command cp ../src/linkmac .)
  4. Change the permissions of the script linkmac to allow it to execute, by doing the command:
      chmod +x linkmac
  5. Then execute the script by typing:   ./linkmac
The result will be that the executables folder will now have a set of links, one for each program, that allow the programs to be executed simply by typing their names. Thus the programs in that folder can then be executed either by clicking on their icon, or by typing their name (in lower case) preceded by ./ to indicate the current folder, such as ./dnaml

This setting up of these links needs to done only once, and they will be available thereafter.

Two problems running our MacOS executables

  1. The executables permission problem: The latest Mac OS operating system versions, since 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. The problem happens because when I made the 3.695 executables, I did not sign them with my Apple Developer identity, so they appear to be from some dangerous person.

  2. The file path problem: When the programs are run on recent versions of MacOS (since Catalina, which is MacOS 10.13) the system may report that it cannot find their default input files "infile" and/or "intree", or that they need to be told where to write the default output files such as "outfile". This is due to a change in the default values of the PATH variables. The solution will be to use not just the name "infile" but the full file paths such as /User/Foobar/phylip/phylip-3.695/exe/infile
To learn how to deal with these problems, look at the detailed instructions in our Bugs documentation page here, and while you're at it, enjoy the image of the world's largest terrestrial true bug.


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 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-3.697.tar.gz
This uncompresses the archive so that it will now be bigger and then extracts the archive. A phylip3.697 folder is created that contains within it three folders, doc, exe, and src, as well as a web page phylip.html. You should start with that web page. It contains links to the documentation web pages, including the main documentation web page main.html.

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 install
which 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 install

If there are problems with the compilation, read the relevant sections of main.html and also the beginning of the Makefile. Note: On some compiles with the GCC compiler you may encounter error messages about multiple definitions, so that it refuses to create the executables. See the Bugs page here for details on how to fix this problem by a single-line change in a Makefile.

With luck this will work. After the compilation the executables and their font files will be in folder exe.

Load Library Path problem.    I have encountered problems with using the Java interface for the Drawgram and Drawtree programs on Linux systems. When running the interface and using its Preview function to preview the tree, there may be an error message saying that the program has been unable to find the library file or These files are present in the executables folder, but the program still cannot find them unless the load library path is specified. This can be done one of three ways:

  1. Before running Drawtree or Drawgram, give a command to specify the path. For example, you were user "ernie" and if the exe folder were the folder /home/ernie/phylip/phylip-3.697/exe you add that to the LD_LIBRARY_PATH variable with the command
    export LD_LIBRARY_PATH=/home/ernie/phylip/phylip-3.697/exe:$LOAD_LIBRARY_PATH
    This has to be done once each session.
  2. Alternatively, you can put that command in the .bashrc or in the .bash_profile file in your home directory (folder) so that it is executed every time you log in.
  3. If you have access to the /etc folder on your system, you could instead put the path /home/ernie/phylip/phylip-3.697/exe in the file /etc/ which informs your program where to search for libraries.
These have been problems in recent versions of MacOS. However, as of MacOS Catalina 10.5.17 these two problems seem to have gone away. If you have either for any recent version of MacOS, do send us an email with details so we can keep the information here current.


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, in the webpage on Old Versions of PHYLIP, just in case anyone needs it.

Downloading the single Stuffit archive

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, seem to regard the executables files as text files, and they try to open them under SimpleText, which of course does not work.

Downloading multiple smaller Stuffit archives

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 .sit. 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:

  1. Move the exe folder inside the phylip folder.
  2. Open the exe.1 folder, and mark all of its files (you can do this using the Select All menu option in the system Edit menu).
  3. Drag this group of marked files into the exe folder which is now inside the phylip folder.
  4. Now do the same for exe.2 (mark the files and drag them into exe).
  5. And do the same for exe.3 (mark the files and drag them into exe).
  6. You can now discard the folders exe.1, exe.2 and exe.3 (if any). If you have four folders named phylip3.65.0.sit, exe.1.sit, exe.2.sit, and exe.3.sit on your desktop, these can be discarded too.
  7. The phylip3.65 folder can now be moved to wherever you want it to be.


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.

You can also read the latest documentation files here at this link.


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.

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