jalview on Linux

[Tamas Rujan]

Daniel John Rigden wrote:
> 
> Hi
> 
> I need to get a good multiple alignment editor working on my Linux
> machine.  I like Jalview but, as a novice, get tangled in the java
> installation.
> 
> Has anyone had success with Jalview on Linux?  What's the secret?!  Or, is
> there a good alternative out there?  Seaview seems to be the best of the
> rest but lacks a lot of Jalview's features.
> 
> Thanks in advance
> 
> Daniel
> 
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> |                       Dr Daniel John Rigden                             |
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Hi John!

It is pretty simple to get Jalview working... 
You have to edit the file Jalview. (this a kind of config and exec file
for the program)
The file has to look like this:
(if you are using bash)
#!/bin/bash   

export CLASSPATH=<the path you have the jalwiew.jar file>
export PATH=$PATH:<the path you have your jalview dir>
export JAVA_EXE=<the path you have java installed>

$JAVA_EXE jalview.AlignFrame $1 File $2 

That´s all.

Alternative is maybe clustalx for linux...


-- 
Tamás Ruján	 Staff Scientist
Epigenomics AG - Bioinformatics R&D
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