Hello,
Is it possible to specify the outgroup for a calculated tree within Jalview? I’ve looked through the documentation and it doesn’t appear to be an option.
Thank you,
Wesley
Hi Wesley,
Is it possible to specify the outgroup for a calculated tree within Jalview? I’ve looked through the documentation and it doesn’t appear to be an option.
You’re correct - unfortunately, there’s no option in the UI. Jalview performs mid-point rooting before the tree is shown, and otherwise, only allows you to manually switch internal node orders (by double clicking the node).
We recommend Archaepteryx if you want to do more detailed tree manipulations. In fact, we have a student here in Dundee working on replacing Jalview’s built in tree viewer with Christian Zmasek’s tool (https://sites.google.com/site/cmzmasek/home/software/archaeopteryx).
Let us know if you need anything else!
Jim Procter.
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On 30/10/2017 18:08, Loo, Wesley Tsekuang wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)