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).
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:
We will have a demonstration on Wednesday of the program BEAST. The main website for BEAST, from which it can be downloaded is here:
They will be alternatives to downloading version 3.695. You can use either version for the PHYLIP lab, but try 4.0 first.
|Operating system||Download||Installing 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||
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.
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.jarThe 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.