[Jalview-discuss] Sort by tree order

[Sebastien MORETTI]

Hi,

we use this parameter for the applet and it does what it should:
	<param name="sortBy"           value="Tree Order" />

But this value does not seem to exist.
Maybe it resets some internal parameters but our multiple sequence 
alignment is build from a guide tree which in most cases has the same 
topology than our phylogenetic tree (Only branch lengths are different)

So, this value allows us to keep the same order than the guide tree and 
in most cases than the phylogenetic tree.

> Hello Albert.
> 
> Albert Vilella wrote:
>> When using Jalview to open an alignment and associated tree, is there
>> any way to automatically sort the alignment
>> by tree order?
> ah - no - but its obvious this would be a good optional default
> behaviour for both the applet and application (e.g. the alignment is
> automatically sorted whenever a new tree is opened). It will be added to
> the feature request list!
> 
> Jim.

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4056
http://bioinfo.unil.ch/