Hi Christophe - hope summer is treating you well ! On Mon Aug 13 17:26:38 2012, Dr. med. Christoph Gille wrote: > 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. _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
