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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

For example, to run jevtrace using a pair of dendogram and alignment files (Muscle, ProbCons, ClustalW/ClustalX, t_coffee), type the following in a terminal window:

java -jar jevtrace.jevtrace <alignment file>

or

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:

c:\java\jevtrace\jevtrace.jar

 

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.

Typing:

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

For example, to run jevtrace using a pair of dendogram and alignment data (Muscle, ProbCons, ClustalW/ClustalX, t_coffee)), type the following in a terminal or MS-DOS prompt window:

java jevtrace.jevtrace <alignment file>

or

java jevtrace.jevtrace <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>

where
<1> = where your java executable resides
<2> = where webmol and jevtrace classes reside (see the installation).

e.g.

c:\jdk1.3.1_05\bin\java.exe -mx1000M -cp c:\java\classes\webmol\;c:\java\classes jevtrace.jevtrace

 

Performance

If out of memory errors are encountered, use something like the 'java -mx1000m' option. Currently there can be peformance issues for dendrograms of more than about 200 sequences .

Protein Structures

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.

 

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Page last modified 05/08/12