FORESTER - a framework for phylogenomics
Version 1.9 (October 2001)
Copyright (C) 1999-2001 Washington University School of Medicine
and Howard Hughes Medical Institute
All rights reserved
----------------------------------------------------------------



The ".tar.Z" file is for Unix and Linux users.
The ".zip" file is for Microsoft Windows users.

Please email me at: zmasek@genetics.wustl.edu
for reporting bugs, comments, suggestions, complaints, ...


1. Obtaining FORESTER (including SDI and ATV)
---------------------------------------------

ftp://ftp.genetics.wustl.edu/pub/eddy/software/

http://www.genetics.wustl.edu/eddy/forester/




2. Unpacking FORESTER
---------------------

Unix, Linux:

  "uncompress forester.tar.Z"

  followed by:
    
  "tar -xvf forester.tar"



Microsoft Windows:

  Use a program such as WinZip to unzip "forester.zip".


In both cases, a new directory named "forester-1.x" will 
be created in your working directory. This directory contains 
all the unpacked files. 



3. Compiling FORESTER
---------------------

Unix/Linux users please note: If "weird" errors occur
(such as "class not found") you might want to inspect your
CLASSPATH with "echo $CLASSPATH". Please make sure it
contains a path to the current directory (".", "./") or a path
to FORESTER. Alternatively, you could use
the "-classpath" option.


 o   SDI programs (requires JDK 1.2 or greater):
 
     "javac forester/tools/*java"


 o   ATVapp (requires JDK 1.2 or greater):

    "javac ATVapp.java"


o   ATVapp_awt (requires JDK 1.1.x or greater,
    this version of ATV is not supported anymore):

    "javac ATVapp_awt.java"


for more detailed information about ATV (esp. ATV Applets)
please refer to ATV_INSTALL.txt




4. Obtaining Java
-----------------

To download JDK 1.3 Standard Edition for Microsoft Windows:
http://java.sun.com/j2se/1.3/download-windows.html

To download JDK 1.2 Standard Edition for Linux:
http://java.sun.com/products/jdk/1.2/download-linux.html

To download JDK 1.2 Standard Edition for Solaris:
http://www.sun.com/software/solaris/java/download.html



5. More Information
-------------------

SDI manual: "SDI_manual.pdf" in directory "SDI_docs"

API specification for FORESTER (HTML): 
  is in directory "forester_API_specification":
  point your browser to "index.html"
  Or online at:
  http://www.genetics.wustl.edu/eddy/forester/forester_API_specification/

Java: http://java.sun.com/



(last modified: 10/04/01)

Christian Zmasek
