[Jalview-discuss] Sort by tree order

[Sebastien MORETTI]

I forgot to say that sequence order in the multiple sequence alignment 
is the same than in the guide tree.

> 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/