*Paup/Phylip

Dan Jacobson DANJ at JHUHYG.bitnet
Wed Jan 29 10:00:47 EST 1992


A request was made for information about other phylogeny programs besides Paup
.  Phylip was mentioned so I am including the readme file from phylip 3.4 in th
is message.  It contains the full instructions on how to get Phylio (sorry that
's Phylip).  Phylip will run on just about antthing - Unix, IBM compat -PC ,
Macintosh, Vax/VMS ...  The documentation that comes with Phylip is EXTENSIVE
and also includes a list of other programs/packages that you can get for phylog
eny and how to get them! (including paup)  Paup is not free - if you really wan
t to know more about paup - see the phylip documentation (main.doc).  Many than
ks go out to Joe for all the work he has done on Phylip to both develope it
and to support it.

Best of luck,

Dan Jacobson

danj at jhuhyg.sph.jhu.edu

=============================================================================


                       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 CompactPro   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 at genetics.washington.edu
                             joe at evolution.genetics.washington.edu
                             joe at 128.95.12.41

Bitnet/EARNET:               felsenst at uwavm
                             felsenst at uwavm.u.washington.edu
                             joe%genetics.washington.edu at cunyvm.cuny.edu
                             joe%genetics.washington.edu at cunyvm
                             joe%genetics.washington.edu at uwavm
                             joe%genetics at 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)-52



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