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Installing PHYLIP 3.6

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Let's assume that you have fetched the appropriate executables archives (if any)for your machine, together with the Documentation and Sources archive.

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These archives are not simply a single executable for generaluse. Instead they are a (large) number of files, squished together intoone file, and thus called an 'archive'. You have to go through a stepwhich involves getting all the files out of the archive and into afolder on your machine.

We will give these instructions for fourdifferent kinds of systems, Windows, MacOS, Linux or Unix systems,Then we will describe how to access thedocumentation after installing the package.

Windows

When you click to download the Zip archive, most recent Windows systemswill open a window which asks whether you want to open the archive withWindows Explorer, or want to Save the archive. Choose to Save it. Itwill be placed in the Downloads folder of your account. There arenow two possibilities:

1. If it has been extracted, a folder called phylip-3.698 (one whichdoes not have the image of a zipper on the folder icon) will also bethere. Move that folder to where you want it to be. Do not try touse the programs or documentation while it is still in the Downloadsfolder.
2. If it has not been extracted, there will be a Zip archive folder (one whichhas 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 onits icon and selecting Extract All from the menu that appears.

   It will create a folder called Phylip-3.698. So ifyou place the archive on the Desktop, it will make that folder there.

After the extraction is done, you will find the phylip-3.698 folderwhich has three folders within it, called doc, exe, andsrc. There is also a web page phylip.html. You shouldread this in your browser, which you can usually do by clicking on the file. It contains links to the main documentationweb page main.html and to the other documentation pages andprograms.

Note: There has been a report that on Windows Vista (specificallythe report was for Service Pack 2 on Home Edition) that if you extract thefiles into a folder that is somewhere under Program Files, they may notwork properly. You can avoid this problem if you extract them into a folderwhich is somewhere in your own folders. Space shooter (jthaboss) mac os.

What to do if the Avast virus-checking software complains: We have hadseveral reports that the Avast virus-checking software will not allow PHYLIP3.695 to be installed because it concludes that it contains a virus. It iscomplaining about our Java front end for program Drawgram (a file calledDrawGramJava.exe). We have had this file checked carefully by ourvirus-checking company, Sophos, and they find no virus there. There is theinvocation of a 'shell' in that Java code that may alarm Avast, which is beingovercautious. If you can extract and install the code on someone else'smachine, one which has differemt virus-checking software, you then may beable 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 failedbecause a Dynamic Link Library (.dll file) is not found. This has happened whenpeople 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 theproblem with finding DLL files persists in spite of you having the correctversion 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 insize, and is compressed; when uncompressed it is several times larger.

It contains what looks like a normal folder called phylip-3.695, butyou should not use the programs while that folder is in the Downloadsfolder. It isimportant that you use a copy of the contents of the disk imageelsewhere on your system.Decide where the folder phylip-3.695 is going to reside, and movethat folder to that new location. Within it is all thesource code, documentation, and executables.

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

Enabling the programs to be run in a Terminal windows by typing theirnames:A set of links can be set up in the exe folder to enable you torun 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 folderof the Applications folder).
2. At the prompt, change to the folder where the PHYLIP executablesare kept. For example, if you have folder phylip-3.695 on yourdesktop, type in the command
   cd ~/Desktop/phylip-3.695/
3. Copy the file linkmac from the src folderto this exe folder (by giving the command cp ./src/linkmac.)
4. Change the permissions of the script linkmac to allow it toexecute, 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 oflinks, one for each program, that allow the programs to be executedsimply by typing their names. Thus the programs in that folder canthen be executed either by clicking on their icon, or by typing theirname (in lower case) preceded by ./ to indicate the currentfolder, such as ./dnaml

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

Two problems running our MacOS executables

1. The executables permission problem: The latest Mac OSoperating system versions, since Mountain Lion, will not run executables of PHYLIPprograms when you click in their icons. It complains that the developername is unknown. This is a security feature. The problem happens becausewhen I made the 3.695 executables, I did not sign them with my Apple Developeridentity, so they appear to be from some dangerous person.
2. The file path problem: When the programs are run on recentversions of MacOS (since Catalina, which is MacOS 10.13) the systemmay 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. Thesolution 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 andUnix

You can easily installPHYLIP and compile it yourself on a Linux or Unix system,provided that you have a C compileron your system. (On some Linux systems and in some recent versions of Mac OSthe C compiler is not installed by default, and you may have tomake 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 folderby itself, getting into that folder, and giving the command

tar -zxvf phylip-3.697.tar.gz

This uncompresses the archive sothat it will now be bigger and then extractsthe archive. A phylip3.697 folder is created that containswithin it three folders, doc,

exe

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, and src, as wellas a web page phylip.html. You should start with that webpage. It contains links to the documentation web pages, including the maindocumentation web page main.html.

To make executables, use your C compiler. It is probably as simple asgoing into the src directory, copying Makefile.unx andcalling the copy Makefile, and then typing the command
which will cause the programs to be compiled and the executables and fontfiles installed inthe exe directory. Alternatively, you can type the command
instead.

If there are problems with the compilation,read the relevant sections of main.html and also the beginning of theMakefile.

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

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Load Library Path problem. I have encountered problems withusing the Java interface for the Drawgram and Drawtree programs onLinux systems. When running the interface and using its Previewfunction to preview the tree, there may be an error message sayingthat the program has been unable to find the library filelibdrawgram.so or libdrawtree.so. These files are present in theexecutables folder, but the program still cannot find themunless the load library path is specified. This can be doneone of three ways:

1. Before running Drawtree or Drawgram, give a command tospecify the path. For example, you were user 'ernie' andif the exe folderwere the folder /home/ernie/phylip/phylip-3.697/exeyou add that to the LD_LIBRARY_PATH variable with the commandThis has to be done once each session.
2. Alternatively, you can put that command in the .bashrcor 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 yoursystem, you could instead put the path /home/ernie/phylip/phylip-3.697/exein the file /etc/ld.so.conf which informs your program where tosearch for libraries.

These have been problems in recent versions of MacOS. However, as of MacOS Catalina 10.5.17 thesetwo 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 notsafe to use it on the Internet as it has not been upgraded to cope withrecent security threats. We no longer distribute Mac OS 8 or 9 executablesfor our most recent versions of PHYLIP. Nevertheless, we do makeavailable a Stuffit (.sit) archive of executables for PHYLIP 3.65, in thewebpage on Old Versions of PHYLIP, justin case anyone needs it.

Downloading the single Stuffit archive

The archives for Mac OS 8, Mac OS 9 Macintoshes are self-extracting archives.If youare fetching the files using a Web browser directly from your Mac, it willprobably automatically invoke Stuffit Expander to unpack the archives intoself-extracting archives. Self-extracting archives are archives with a smallself-extraction program on their front, so that when they are run asprograms they write a great many files into a folder.

Our default distribution is of a single large (4.9 Megabyte) Stuffitarchive called phylip3.65.sit. This should automatically beunstuffed 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 unstuffedarchives. Recent versions of Mac OS 9, and also the Classic environment underMac OS, seem to regard the executables files as text files, and they try toopen 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 fourarchives. This might be necessary, for example, if you wanted totransfer them to a machine that was not connected to the Internet, and neededthem 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 selfextracting archives willbe 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 putfolders on the desktop. One is called phylip and containsfolders doc and src as well as a web page phylip.html.There are 307 files in all, as these include the documentation files, sourcecode files, and compilation support files. You may have to be patientwhile 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 thisusing the Select All menu option in the system Edit menu).
3. Drag this group of marked files into the exe folder which isnow inside the phylip folder.
4. Now do the same for exe.2 (mark the files and drag them intoexe).
5. And do the same for exe.3 (mark the files and drag them intoexe).
6. You can now discard the folders exe.1, exe.2 and exe.3 (if any). If youhave four folders named phylip3.65.0.sit, exe.1.sit,exe.2.sit, and exe.3.sit on your desktop, these canbe discarded too.
7. The phylip3.65 folder can now be moved to wherever you want it tobe.

Reading the documentation

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The main folder contains a web page, phylip.html. Youshould start by reading it (either by clicking on it to activate yourbrowser, or calling it to the attention of your browser in some other way suchas drag-and-drop). It contains links to the documentation web pages, includingthe 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

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Executables packages are also available from others. For the moment, theseare for earlier versions of PHYLIP (such as 3.61 and 3.68). Theyinclude executables for Red Hat Linux, Debian Linux, NetBSD Unix forIntel-compatible processors, and FreeBSD Unix. For links seeour downloads page.