SISG module 12 (2014) programs

(Where is the main 2014 SISG module 12 web page? It is in the folder above this one, namely here).

PAUP*, some materials for PAUP* labs, including data sets, and some MrBayes lab material

Mark has made available a link for the version of PAUP* that we will use, as well as materials for the PAUP* labs, and data sets for them. There are also links there for other programs: MrBayes, Figtree, and Tracer. These materials are at this link:

http://phylo.bio.ku.edu/sisg2014/index.html

The BEAST program

We will have a demonstration on Wednesday of the program BEAST. The main website for BEAST, from which it can be downloaded is here:

http://beast.bio.ed.ac.uk/software/

PHYLIP 4.0 programs

For the PHYLIP exercises on Monday and Tuesday, you should have PHYLIP installed on your laptop (it will not work on a tablet). The current distributed release is version 3.695, but here we will try out some programs from version 4.0, which is not yet released.

They will be alternatives to downloading version 3.695. You can use either version for the PHYLIP lab, but try 4.0 first.


Downloading and installing the programs

Operating systemDownloadInstalling it
Windows Click here to download the Zip archive On downloading, this archive may be extracted. If not, right-click on it and select the option to extract the archive. Make sure to put all the contents in a folder whose name you will recall (such as phylip).
Mac OS X Click here to download a .dmg archive Then click on the archive icon to open the Disk Image "disk". Click on that to open its folder. Inside you will find a folder named "phylip-4.0sisg". Do not use that there, but copy it to some other place on your disk where you will be able to find it.
Linux Click here to download a .tar.gz archive
  1. Move this to an appropriate place in your folders.
  2. Unpack it by opening a Terminal window and using the cd command to move there, then type the command
    tar -zxvf phylip-4.0sisg.tar.gz
    That should give you a folder phylip-4.0sisg. Within it, the executable programs and their Java interface code will be in folder programs.
  3. If you have a 64-bit Intel-compatible processor in your computer, you should be able to use those executables. If not, see Joe. You could always download and compile the 3.695 version.


Getting the Java front ends of the programs to run on your computer

For PHYLIP we are making available a pre-alpha pre-release copy of 9 of the PHYLIP programs from PHYLIP 4.0. These use a Java front end which requires that you have a recent version of Oracle Java.

Note that two programs in version 3.695, Drawgram and Drawtree, also require a recent version of Oracle Java. However it is not essential to use those two programs to complete the lab exercise.

Windows:
For Windows machines Oracle Java can be installed rather easily with a free download from the main Java web site. There is a link to download and install Oracle Java on the SISG Computing and Software web site, in the links for our module, to that web site.
Mac OS X:
For Mac OS X machines the version of Java that is provided with the Mac OS X operating system should be good enough, so you do not have to install Java yourself.
Linux:
However if you have a Linux system, particularly an Ubuntu Linux system, things may or may not be more difficult. Ubuntu Linux has its own Java which may be able to run the PHYLIP Java code. Try this, to see if it works with the PHYLIP Java code. If not, with some difficulty it is possible to download a recent Oracle Java to an Ubuntu Linux system, and configure the paths properly to use it. 3.695. Below see more on how to set up Oracle Java on Linux.


Here are more details of how to set up Oracle Java on Linux:

The script that sets up the Linux environment and start the Java interface is named ...Java.unx. Because nobody without root privileges can install anything on a Linux machine where any other user can see it, we had to write the Java execution scripts so that it looked for Java locally in the user's directory. So for each Java script (DrawGramJava,unx for example) there is an execution script which set up the environment that reads:

export PATH=~/jdk1.7.0_11/bin/:$PATH
export JAVA_HOME=~/jdk1.7.0_11/bin/
export LD_LIBRARY_PATH=.
java -jar ./DrawGram.jar
The user must replace the ~/jdk1.7.0_11 with the path to Oracle Java on their machine. Then they double click on the ...Java.unx file and the Java interface will run.