GETTING PHYLIP 3.4 BY ftp Anyone with an Internet connection can now get PHYLIP 3.4 (my package of computer programs for inferring phylogenies) using "anonymous ftp". Here's how to get it: PHYLIP sources and executables exist for ftp distribution in three forms. One is as "compressed tar archives", a system of storing many files as one file and then compressing the size of the file that is used in Unix systems. Another is as "self-extracting Zoo archives", a similar archiving system used on PCDOS systems. A third is as "self-extracting archives" created by CompactPro, an archiving program used on Macintoshes. The names of the archives are Archive Form Name ------- ---- ---- Sources and docs Compressed tar phylip.tar.Z PCDOS executables Compressed tar phylipxp.tar.Z Macintosh executables Compressed tar phylipxm.tar.Z Sources and docs Self-extracting Zoo phylip.exe PCDOS executables Self-extracting Zoo phylipxp.exe Sources and docs Self-extracting CompatcPro phylip.sea.bin Macintosh executables Self-extracting CompactPro phylipxm.sea.bin You will only want to get PHYLIP in one of the three forms. To extract the Compressed tar archives you need to use the utilities "uncompress" and "tar" which are standard on almost all Unix systems. Other mainframe or workstation operating systems may have utilities to do the uncompression and the extraction of these archives. To extract the self-extracting Zoo archives, you can simply put them in a (big enough) directory on a PCDOS machine, and execute the archive as if it were a program! It contains its own extraction program and will extract the separate files from the archive on its own! The self-extracting CompactPro archives were transferred to my workstation using the MacBinary protocol (hence the ".bin" suffix) and with the "binary" mode of ftp set. They should be downloaded to a Macintosh using the "binary" setting (if relevant) and the MacBinary protocol. They can then be extracted using the CompactPro archiver, or ... you can simply put them in a (big enough) disk area on a Macintosh and double click on them. They will then present an opportunity to choose the directory the files go into, and on clicking on the "Extract" button will unstuff themselves into a number of subdirectories and many files. How to Transfer the Files by ftp Here is how to use ftp to transfer the archives and how to extract the files from them: 1) Make sure you have enough room for PHYLIP on your system. The compressed tar archive containing the package (the source code and documents) is phylip.tar.Z, which is over 850K in size. After it is uncompressed, it is almost 2.7 Megabytes in size. The archive phylipxp.tar.Z containing the the PCDOS executables is almost 975K in size and when uncompressed is about 1.6 Megabytes. If you are instead going to get the Zoo archives, these are 1.0Mb and 1.1 Mb in size, and when uncompressed about 2.75 and 1.6 Megabytes. The Macintosh CompactPro archives are 750K and 740K in size and extract into about 2.6 and about 1.6 Megabytes. Whichever of the three systems you are using, you will probably need as much space as the sum of all four of these numbers (the two archive sizes and the sizes of the two sets of resulting files). 2) Use your local system's version of FTP to connect to my system, which is evolution.genetics.washington.edu. If your system says it has never heard of this address, try the number 128.95.12.41 instead. Alternatively, try Alan Rogers' system, anthro.utah.edu (if your system says it has never heard of anthro.utah.edu, try the number 128.110.192.93 instead). 3) In response to the "Name" or "Login" prompt, type "anonymous". In response to the "password:" prompt, type your last name. If you are using ftp from a VAX VMS system you may have to type USER followed by "anonymous" to get to log in. 4) Once logged in, change into the directory "pub" by typing "cd pub". (On some systems the command may instead be "cwd pub".) 5) Give the appropriate command to tell ftp that the data will be binary (on my system you type "binary"). 6) To get the package, tell ftp to get the file phylip.tar.Z (on my system you type "get phylip.tar.Z"). To get the PCDOS executables, get the file phylipxp.tar.Z. If you are getting the Zoo archives instead, type "get phylip.arc" and "get phylipxp.arc" instead. The fifth file in this directory, "phylip.read.me" is these instructions. 7) Get out of ftp. (On my system you type "quit") 8) If you are (say) going to move the Zoo archives to a PCDOS system by a file transfer program such as Kermit, that can now be done, keeping in mind that both archives are binary (not text) files and need to be transferred using the same methods as you would use for an executable program. 8) (Macintosh CompactPro archives only). You can use a file trasfer program to move the CompactPro archives to a Macintosh, but make sure that you enable the "MacBinary" mode which transfers binary files with all their attributes intact. If you use ftp to transfer the CompactPro archives to your Mac, make sure you also have the "image" (or "binary") mode set (as well as the MacBinary, mode so that the files transfer properly. If you use Versaterm to do the transfer to your Mac, make sure that you select "binary" in BOTH the "file" and "kermit commands" menus. To extract the archives simply place them in a disk area that has enough space and then double-click on the file. It will present a dialog box asking where the files should be put. Work your way through the directories, clicking appropriately, until you reach the one where you want them to go. Then click on "Extract". It should self-extract and form a number of folders. NOTE -- If you try to run the Macintosh version of the programs by simply double-clicking on them, but you do not provide in the same directory an input file of the correct name (such as "infile") they will crash with a mysterious error message about an "unimplemented trap". Be sure you have the input file or files of the proper name (or names) in the proper place. 9) (Zoo archives only): Put each of the two archives in its own directory on a PCDOS system, and simply execute it as a program (i.e., for the file phylip.exe just type PHYLIP). The archive will self extract and a series of files will appear in the directory. At this point you have succeeded. 9) (Tar archives only): If you are on a Unix system you will probably have a utility called "uncompress". Create and new directory and move phylip.tar.Z (or phylipx.tar.Z) into it. You can simply issue the command: "uncompress phylip.tar.Z" (and/or "uncompress phylipx.tar.Z"). When the command terminates you will find a file called "phylip.tar" (or "phylipx.tar") in your directory. The original compressed tar archive(s) will be gone. 10) (Tar archives only): Unix systems also have a utility called "tar" that can unpack the archives phylip.tar and phylipx.tar. The command is most likely: "tar -xvf phylip.tar" or "tar -xvf phylipx.tar". These will cause the files to be unpacked and placed in the current directory. If you do not have uncompress you will have to use pdtar or zcat instead. If you have pdtar (Public Domain TAR), you can do this by typing "pdtar zxvf phylip.tar.Z" on your system. If you have zcat, type "zcat phylip.tar.Z | tar xvf -". If this doesn't work, consult your local "guru", who may be able to tell you how to uncompress and unpack. 10) If you get the PCDOS executables onto a non-PCDOS system, remember that these are binary files and that when you transfer them to a PCDOS system you must make sure that the file transfer program is set up to correctly transfer binaries. 11) REGISTER YOUR COPY. Send electronic mail to me telling me that you have PHYLIP 3.4, that you got it by anonymous ftp, and also tell me: Your name and address (no more than 5 lines) Your telephone number and electronic mail address (if any) Name of your computer, operating system, and Pascal compiler (if any) My email addresses are: Internet (NSFNET, ARPAnet): joe@genetics.washington.edu joe@evolution.genetics.washington.edu joe@128.95.12.41 Bitnet/EARNET: felsenst@uwavm felsenst@uwavm.u.washington.edu joe%genetics.washington.edu@cunyvm.cuny.edu joe%genetics.washington.edu@cunyvm joe%genetics.washington.edu@uwavm joe%genetics@uwavm UUCP: ... uw-beaver!evolution.genetics!joe ... uw-beaver!hilbert.ms!evolution.genetics!joe and my phone numbers are: Work: (206)-543-0150 Home: (206)-526-9057 Those of you on non-Unix systems may have some trouble, since tar is not universally available. There are a number of free versions out there, however, so you may be in luck. If you would care to port pdtar to your local system, you can get the source free from John Gilmore, Nebula Consultants, PO Box 170608, San Francisco, California, USA 94117-0608 whose e-mail address is: hoptoad!gnu or gnu@toad.com I am grateful to Alan Rogers of the University of Utah for initiating the anonymous ftp version of PHYLIP and writing part of this document. He can be reached at rogers@anthro.utah.edu and his postal address is: Alan Rogers, Department of Anthropology, University of Utah, Salt Lake City, UT 84112 and his phone is (801) 581-5529. Joe Felsenstein Department of Genetics SK-50 University of Washington Seattle, Washington 98195, U.S.A.