How to FTP the Lamarc package

Revised April 27, 1994

This directory contains files relating to the LAMARC package.  The
programs are designed to estimate population parameters such as
population size and mutation rate from a sample of nucleotide
sequences using Metropolis-Hastings sampling.

-----------------------------
Programs available:

COALESCE -- Estimate 4 x population size x mutation rate in populations
without migration, selection, or recombination.  This program is
distributed as a compressed, tarred archive called coalesce.tar.Z and
must be extracted and uncompressed.  The archive contains C source code,
documentation in ASCII formats, sample input, output and parameter
files, and a Makefile.  A separate file, coalesce.hqx, contains MacIntosh 
executables.

FLUCTUATE -- Estimate 4 x population size x mutation rate, and
exponential growth rate, in populations without migration, selection, or
recombination.  This program will emulate COALESCE and we will
eventually stop distributing the former program.  The compressed, tarred
archive is called fluctuate.tar.Z.  A separate file, fluctuate.hqx,
contains Mac executables.

Papers available:

Metro-Hastings -- A general description of the method.  This paper is in
LaTeX format, compressed, in the file metro-hastings.tex.Z.

-----------------------------

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 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 full e-mail address.  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.  It is important that
the password you type be a proper e-mail address, preferably your Internet
address.

  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 "lamarc" by typing "cd lamarc".  (On some
systems the command may instead be "cwd lamarc".)

  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.  These instructions will use the coalesce program as an
example; for others, substitute the appropriate name.

  8) To get the compressed tar archive version of the package, tell ftp to get
the file coalesce.tar.Z (on my system you type "get coalesce.tar.Z"). 

  9) Get out of ftp. (On my system you type "quit")

  10) If you are on a Unix system you will probably have a utility 
called "uncompress".  Create a new directory and move the archive (say 
coalesce.tar.Z) into it.  You can simply issue the command: "uncompress 
coalesce.tar.Z".  When the command terminates you will find a file
called "coalesce.tar".  The original compressed tar archive(s) will be gone.

  11) (Files ending in .tar only)  Unix systems also have a utility called 
"tar" that can unpack archives like coalesce.tar.  The command is most likely:
"tar -xvf coalesce.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
coalesce.tar.Z" on your system.  If you have zcat, type
"zcat coalesce.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.

 12) REGISTER YOUR COPY.  Please send electronic mail to me indicating
which program(s) and versions you have, and giving your regular and 
electronic mail addresses so that I can reach you with bug fixes and
other information.  My Internet addresses (the first one is preferred):

mkkuhner@genetics.washington.edu
mkkuhner@phylo.genetics.washington.edu
mkkuhner@u.washington.edu

Mary K. Kuhner
Department of Genetics SK-50
J255 Health Sciences
University of Washington
Seattle, WA 98115, USA
(206) 543-8751
