Sort by tree order

Jalview Discussion
1

Hi,

When using Jalview to open an alignment and associated tree, is there any way to automatically sort the alignment
by tree order?

Cheers,

Albert.

2

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.

3

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

4

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

5

Hi Sebastien.

Sebastien MORETTI wrote:

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.

It seems you are correct there! I just checked the V2.4 source
thoroughly, and that value of the sortBy parameter will have no effect.

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.

For most multiple sequence alignment programs, the guide tree would tend
to reflect the final alignment ordering and since JalviewLite will not
re-order the alignment unless a valid sortby parameter is provided, the
displayed ordering is always as specified in the alignment file.

Jim.

···

---
The University of Dundee is a Scottish Registered Charity, No. SC015096.

6

Sebastien MORETTI wrote:

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

sorry for over-posting from your early message, Sebastien.

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

I also forgot to say that I think this will probably be exactly how the
'sort by tree order' option will be enabled for the applet when the
feature is added.

Jim

···

--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.