Getting Started (with Jevtrace2, i.e. v3.12b. or greater)
On some systems (e.g. Windows) with newer Java installations (1.4 or higher) it is possible to execute Jevtrace by double-clicking on the JAR file.
Otherwise the program needs to be started through a command (typed in a terminal window, or stored in an alias or shortcut). Assuming your working directory is the same directory that holds the JAR file, to see the complete Jevtrace startup options type the following in a terminal window:
java -mx1000M -jar jevtrace.jar jevtrace.jevtrace -help
java -jar jevtrace.jevtrace <alignment file>
java -mx1000M -jar jevtrace.jar jevtrace.jevtrace <dendogram file> <alignment file>
The above command line examples assume you are in the same directory as the Jevtrace JAR file. Otherwise you will need to specify a full path to the JAR file:
java -mx1000M -jar <full path to JAR file> jevtrace.jevtrace
Where the full path will look something like:
Getting Started (with Jevtrace versions prior to 3.12b)
Step 2 of the installation allows convenient command line execution of the jevtrace package from any directory on your system.
java jevtrace.jevtrace <options>
will start the program with a demonstration alignment and dendrogram. Beginning with version 2.2, jevtrace can load data after startup (even with demo data), either a dendrogram/multiple sequence alignment pair, or just a multiple sequence alignment.
To see the complete jevtrace startup options type the following in a terminal window:
java jevtrace.jevtrace -help
java jevtrace.jevtrace <alignment file>
<dendogram file> <alignment file>
(Mostly Windows or Mac) Startup Problems
If you are having trouble with setting up the CLASSPATH variable etc., things can be made to work as long as you know where the java executable and the jevtrace classes are.
This command line will always do the job:
<1> -mx1000M -cp <2> jevtrace.jevtrace <options>
c:\jdk1.3.1_05\bin\java.exe -mx1000M -cp c:\java\classes\webmol\;c:\java\classes jevtrace.jevtrace
If out of memory
errors are encountered, use something like the 'java -mx1000m' option.
Currently there can be peformance issues
of more than about 200 sequences .
Protein structures in the PDB format can be opened from within jevtrace by clicking (shift-clicking in Jevtrace2) on the appropriate sequence name and clicking on the 'Open WebMol' button. The sequence of the PDB will be aligned with the selected sequence in the multiple alignment and WebMol will display the structure.
Email bugs, comments, suggestions: