[EMBOSS] SeaView

[David Martin]

On 18/7/08 13:48, "Guy Bottu" <gbottu at vub.ac.be> wrote:

> Staffa, Nick (NIH/NIEHS) wrote:
>> I would really appreciate any evaluation of the editor SEAVIEW by anyone
>> reading this.
>> Do you think SeaView is as good as SeqLab
> 
> Dear Nick,
> 
> Well, at the BEN site I installed SeaView as replacement, when we lost
> GCG+SeqLab. SeqLab does multiple sequence editing + graphical display of
> features + allows to execute programs on sequence (ranges). SeaView is
> basically 
> just an editor (although it can call clustal or muscle to re-align portions of
> the aligment, and make a dotplot). What I find a great loss is that in SeqLab
> you can with the mouse select a block and then with one click delete it, while
> with SeaView you need to press as many time the <backspace> as there are
> columns 
> to delete. But if you have nothing else SeaView is certainly not bad. It has
> the 
> advantage to be freeware and that there are versions for several platforms.
> You can install it and test it yourself. It is in principle easy to install
> (although there might be problems with prerequisite libraries). You can obtain
> it from ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview (and in some LINUX
> distributions like Gentoo it is actually vailable). If you run into trouble I
> am 
> willing to give some advice.

You might want to take a look at Jalview 2 which will do editing, MSA,
feature display and more. OK, I am a little biased (it is developed in our
group) but a quick rundown of the key features:

* edit on blocks/ranges
* edit using representative sequences
* Multiple views on the same alignment
* features from arbitrary DAS servers (even map protein features onto DNA.)
* integration with jmol for structure viewing
* hide/display arbitrary columns/rows.
* Multiple sequence alignment (Clustal, MAFFT, Muscle)
* Tree construction on arbitrary regions.

Available from Jalview.org

..d


-- 
David Martin PhD
Post-Genomics and Molecular Interactions Centre
University of Dundee
http://www.compbio.dundee.ac.uk/
The University of Dundee is a registered Scottish charity, No: SC015096