GETTING PHYLIP 3.5 BY ftp Anyone with an Internet connection can now get PHYLIP 3.5 (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 PCDOS archives. A third is as self-extracting archives created by CompactPro, an archiving program used on Macintoshes. The names of the available archives are Contents Form Name -------- ---- ---- C Sources and docs Compressed tar phylip.tar.Z Pascal Sources and docs Compressed tar phylipp.tar.Z C Sources and docs PCDOS Self-extracting phylip.exe Pascal Sources and docs PCDOS Self-extracting phylipp.exe PCDOS executables PCDOS Self-extracting phylippx.exe, phylippy.exe 386 PCDOS executables PCDOS Self-extracting phylip3x.exe, phylip3y.exe 386 Windows executables PCDOS Self-extracting phylipwx.exe, phylipwy.exe, phylipwz.exe C Sources and docs Self-extracting CompactPro phylip.sea.bin Pascal Sources and docs Self-extracting CompactPro phylipp.sea.bin Macintosh executables Self-extracting CompactPro phylipmx.sea.bin You will only want to get PHYLIP in one of the three forms of archive, and generally you will need one of the two kinds of the Sources and documentation files, as the executables archives have essentially no documentation in them. 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. We do not any longer distribute separate executables for Sun, SGI, and DECstation systems as the C source code of the package compiles easily on those systems using the "make" utility. To extract the self-extracting PCDOS 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! Each 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. Most of the archives are compressed by a factor of 2-3, so that you will need enough space on your system to hold each archive (at least temporarily) plus the the files it extracts into. Thus if an archive is 1090k in size you may need 1090k+3270k of disk space to extract it, 3270k being needed permanently. Once you have connected to my machine by ftp, you will be able to see the archive file sizes by issuing a DIR command and can calculate whether you have enough space for the archives you want. 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. 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 or from some Telnet programs you may have to type USER followed by "anonymous" to get to log in. 4) Once logged in, move into the directory "pub" by typing "cd pub". (On some systems the command may instead be "cwd pub".) 5) Move into the subdirectory "phylip" by typing "cd phylip". (On some systems the command may instead be "cwd phylip".) 6) Give the appropriate command to tell ftp that the data will be binary (on my system you type "binary"). 7) Look at the above list of archive names and types and decide what you want to get. If you are to get executables, make sure you also will get the source code and documentation archive. 8) To get the compressed tar archive version of the package, tell ftp to get the file phylip.tar.Z (on my system you type "get phylip.tar.Z"). To get the 386 PCDOS executables you will want to get four archives: the source code and documentation archive and three executables archives. Thus you might for example issue the commands: get phylip.exe get phylip3x.exe get phylip3y.exe get phylip3z.exe Similarly for the generic PCDOS version, the 386 Windows version, or the Macintosh executables, you would issue commands to get the source code and documentation archive plus several executables archives. 9) Get out of ftp. (On my system you type "quit") 10a) If you are (say) going to move the self-extracting PCDOS archives to a PCDOS system by a file transfer program such as Kermit, that can now be done, keeping in mind that the archives are binary (not text) files and need to be transferred using the same methods as you would use for an executable program. Similarly, if you are instead using Internet to transfer the archives from one machine to another, use the "binary" mode for the transfer. 10b) (Macintosh CompactPro archives only). You can use a file transfer 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. 11a) (PCDOS self-extracting 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. If all files were written you can now delete the archive to save space. 11b) (Tar archives only): If you are on a Unix system you will probably have a utility called "uncompress". Create and new directory and move the archive (say phylip.tar.Z) into it. You can simply issue the command: "uncompress phylip.tar.Z". When the command terminates you will find a file called "phylip.tar". The original compressed tar archive(s) will be gone. 12) (Tar archives only): Unix systems also have a utility called "tar" that can unpack archives like phylip.tar. The command is most likely: "tar -xvf phylip.tar" (or analogously for other archive names). It 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. 13) REGISTER YOUR COPY. Send electronic mail to me telling me that you have PHYLIP 3.5, which language (C or Pascal) you got the source code in, and which version of the executables you got, that you got these by anonymous ftp. and also tell me: Your name and address (no more than 5 lines) Your telephone number and electronic mail address (1 line total) Name of your computer, operating system, and C or Pascal compiler (1 line) These should start in column 1 and fit into the required number of lines to make it easier for me to record them in my user database. 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@uwavm joe%genetics@uwavm UUCP: ... uw-beaver!evolution.genetics!joe and my phone numbers are: Work: (206)-543-0150 Home: (206)-526-9057 I am grateful to Alan Rogers of the University of Utah for initiating the anonymous ftp version of PHYLIP and writing part an earlier version of this document, and to Don Gilbert and Steve Smith for help with earlier versions of the archives. Joe Felsenstein Department of Genetics SK-50 University of Washington Seattle, Washington 98195, U.S.A.