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To: bionet-biology-computational@net.bio.net
From: Tamas Rujan <rujan@epigenomics.com>
Newsgroups: bionet.biology.computational
Subject: Re: jalview on Linux
Organization: Epigenomics AG
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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
> 
> +-------------------------------------------------------------------------+
> |                       Dr Daniel John Rigden                             |
> | CENARGEN/EMBRAPA                 | e-mail: daniel@cenargen.embrapa.br   |
> | Parque Estacao Biologica         | http://www.cenargen.embrapa.br       |
> | PqEB - Final - Av. W3 Norte      |  Phone:  +55 (61)448-4741            |
> | 70770-900, Brasilia-D.F.-BRAZIL  |  Fax:    +55 (61)340-3658            |
> +-------------------------------------------------------------------------+

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
Kleine Präsidentenstraße 1	Tel.: +49-30-24345-354   
Berlin  10178 Germany		Fax.: +49-30-24345-555


.