Hi Christophe - hope summer is treating you well !
I like Jalview's excellent inter-connection of the alignment view
and the phylogenetic tree view.
Therefore I would like to use Jalview as a
display option for another Java application. After launching
Jalview via Java Webstart, I want it to display the sequence
alignment plus the evolutionary tree derived from that alignment.
Shouldn't be a problem.
I understand from the docs that I need to use the program option
"tree" followed by a tree file. Is it difficult to make such tree
file? What kind of format is it.
Jalview reads newick format tree files - these are generated by most of the phylogeny programs around (some create NHX - new hampshire extended, which jalview can cope with, but some create NEXUS files, which Jalview currently cannot read).
Can it be generated with
clustalw or with jalview itself?
ClustalW creates a .dnd file - you can pass this to Jalview along with the alignment created by ClustalW and that would work. The tree ClustalW creates is not really an evolutionary tree, though - it's the guide tree used to create the MSA.
Or can Jalview take care
of making this file which would be most convenient.
You could pass a groovy script to Jalview using the '-groovy' option - that would trigger tree generation using Jalview's built in tree generation function, but it might probably easier to run a phylogeny program from your own program to create the tree (preferably phyml or mrbayes, but paup, phylip, etc will also do what you want).
There are loads of options here - it very much depends on what you want to show (real evolutionary tree vs clustering based on alignment, or something else, like structural similarity...).
Jim.
ยทยทยท
On Mon Aug 13 17:26:38 2012, Dr. med. Christoph Gille wrote: