Project: CIPRes 
Version: "Developer 1.0"
Company: San Diego Supercomputer Center

Description:
This platform has been created for completing phylogenetics analyses.

The features in the current release include:
	- implementation of the recursive-iterative DCM3 tree improver algorithm.
	- record commands and create playback scripts.
	- set default directory for nexus and script files.

Hardware and software requirements:
	- Requires java version 1.4.2_04 or greater installed on your machine.
	- Use of recidcm3 requires:
		- Tree searching software.  At least one of the following:
			- paup (available at http://paup.csit.fsu.edu/)
			- raxmlHPC is optional.
		- Python
			- version 2.4 is recommended (see "Directions for upgrading to 
				python 2.4" below). Python 2.4 is required if you are running
				on a Mac with an operating system version before 10.4.

Installation/Launch instructions:
	- Uncompress the downloaded tar or zip file
	- The uncompressed directory can be stored anywhere on your machine as long as the 
	  hierarchy inside the cipres folder is kept intact
	- On windows, double-click bin\cipres.bat to launch.  On the mac or unix, run
	  bin/cipres.sh to launch.
	- The first time the application is launched you may be prompted to enter 
	  Tools > Preference Setter and specify the locations of the paup, python and
	  raxml executables on your machine.  You won't be prompted if the application
	  is able to find them in your PATH environment variable.
    - If you don't have raxml, edit resources/cipres_config.properties.  Find the 
	  line that says "# cipres.registry.raxml.not.used=1" and remove the # to
	  uncomment the property.  Raxml will still show up as a choice in the recidcm3
	  gui and you must avoid choosing it!


Directions for upgrading to python 2.4:
	- navigate to http://undefined.org/python
	- follow the links "announcement" > "PantherPythonFix" > "PantherPythonFix.dmg" for the download 
	- install MacPython-OSX-2.4.2-1.dmg from http://undefined.org/python.
	- Note: By default this leaves python 2.3 in /usr/bin/python and puts a link to the python2.4 
	  executable at /usr/local/bin/python.   Enter the latter path (/usr/local/bin/python) when in 
	  the cipres application at Tools > Set Preferences > Python Path.



Troubleshooting:

Recidcm3 Performance (times are approximate):

OS	        processor	       ram	      file size(#taxa)    time to do 1 iteration
_______     ________________   ______     ________________    ______________________

Mac OSX     PPC G4 1.5GHz      1Gig       49                   4 sec       
                                          500                  6 sec
									      7180                 4.5 min

Win XP      Pentium M 1.7GHz   1Gig       49                   4  sec
                                          500                  4  sec
										  7180                 4.5 min

  
Contact us at:

http://www.phylo.org
TODO: Report bugs at:
http://ngbugz.sdsc.edu/ 

Date: June 8, 2006

Copyright 2006  The Regents of the University of
California on behalf of the San Diego Supercomputer Center All Rights
Reserved

Permission to use, copy, modify and distribute any part of this CIPRes
software for educational, research and non-profit purposes, without fee, and
without a written agreement is hereby granted, provided that the above
copyright notice, this paragraph and the following three paragraphs appear
in all copies.

Those desiring to incorporate this CIPRes into commercial products or use
for commercial purposes should contact the Technology Transfer &
Intellectual Property Services, University of California, San Diego, 9500
Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815,
FAX: (858) 534-7345, E-MAIL: invent@ucsd.edu.

IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR
DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
LOST PROFITS, ARISING OUT OF THE USE OF THIS CIPRes, EVEN IF THE UNIVERSITY
OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE CIPRes PROVIDED HEREIN IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
CALIFORNIA HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES,
ENHANCEMENTS, OR MODIFICATIONS.  THE UNIVERSITY OF CALIFORNIA MAKES NO
REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER IMPLIED OR
EXPRESS, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE
CIPRes WILL NOT INFRINGE ANY PATENT, TRADEMARK OR OTHER RIGHTS.