Hi
It seems that Jalview cannot view uprooted tree. Are you going to develop it?
I need this function.
Thanks
Jeff
Hi, Jeff.
In my experience, Jalview is most powerful when it comes to visualizing sequence alignments.
For tree manipulation, I’d recommend the program FigTree.
Cheers!
-Joel
···
On Mon, Jun 13, 2011 at 12:27 PM, Chen, Xianfeng (CDC/OID/NCIRD) (CTR) <vbx7@cdc.gov> wrote:
Hi
It seems that Jalview cannot view uprooted tree. Are you going to develop it?
I need this function.
Thanks
Jeff
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Hi Jeff.
In my experience, Jalview is most powerful when it comes to visualizing sequence alignments.
Joel's right here. Jalview will happily read an unrooted tree - but it will only display rectangular dendrograms. Jalview's treeviewer is really only designed for interactive analysis of alignments, and is missing most of the nice features of modern phylogenetic visualization tools (radial/angular layouts, label editing, phyloXML and nexus support, etc). So of you need this, you need to look elsewhere. In addition to FigTree, there are a whole bunch of other tools you might want to use - depending on what you want to do (e.g. Archeopteryx, Dendroscope, SplitsTree, ARB, etc).
Jim.
···
On 13/06/2011 20:33, Joel Guenther wrote:
Thanks for your kindly response.
you're very welcome !
Jalview is perfect in presenting alignment, but I want to sub-group sequences in multialignment based on their similarity, in the other words, I will take look at the phylogenetic tree and decide what sequences to be selected, therefore I need to know some parameters building the tree. Dendroscope and others are good tree viewer, but could allow you to sub-group sequence and re-multiple-alignment.
Ah - I see, so Jalview is certainly what you want. However, it sounds like you should calculate the tree using another program and import it onto the source alignment in Jalview (which is probably what you are doing already). You can then use Jalview's tree-based subgrouping features to explore the variation and conservation patterns between the subgroups (there's an exercise in chapter 2 of the jalview manual at http://www.jalview.org/tutorial/TheJalviewTutorial_screen.pdf that covers this).
Co-incidentally, I have been in a few discussions with people here in Dundee about introducing 'real' phylogenetic methods into Jalview, and hope that we'll have at least one phylogenetic method available in a release by the end of the year. Until then, you'll have to use another program to calculate a reliable tree. For this, I'd normally prefer to use TOPAli or SplitsTree - which both allow trees to be saved in newick format for import to Jalview.
Happy jalviewing!
Jim.
···
On 24/06/2011 18:57, Chen, Xianfeng (CDC/OID/NCIRD) (CTR) wrote: