[Jalview-discuss] Alignments

[Geoff Barton]

Dear Héctor,

Sorry you have been having problems doing alignments in Jalview. I've just tried it, it was slow, but did come back with an alignment.

There were some problems with our cluster over the last few days which may have caused what you are seeing. Please try again and ideally post your experience on the jalview-discuss mailing list.

Incidentally, were you aware that you can do the alignments locally by installing JABAWS? For instructions, please see: www.compbio.dundee.ac.uk/jabaws<http://www.compbio.dundee.ac.uk/jabaws>.

With thanks,

Geoff.

On 16/03/2018 11:52, Héctor Montero wrote:
Hello, I want to align 37 sequences (input by plain text) in Jalview using the function Muscle by default. When I do this, the job appears a queuing endlessly and after a while, an error message appears. This does not happen when I input a few sequences. So I want to ask you how can I instead input an alignment already performed in Muscle into Jalview. Apparently I cannot just copy and paste the results I got in Muscle because they are not continuous.
Thanks
Hector

--
Héctor Montero Sommerfeld



--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | ***@dundee.ac.uk<mailto:***@dundee.ac.uk>
Tel: [phone] | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton


The University of Dundee is registered Scottish charity: No.SC015096


The University of Dundee is a registered Scottish Charity, No: SC015096

[Geoff Barton]

Hi Héctor,

This training video should help you get your alignment into Jalview.

Jalview has a youtube channel with many videos that explain basic and advanced Jalview functions, so this is usually a good place to start for help.

The full list of videos is on this link:

https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw

If you have further problems, please join the jalview-discuss mailing list and post your questions there.

All the best,

Geoff.

P.S. we are still working on the problem you reported with Muscle in Jalview. Hopefully this will be resolved soon. It usually works reliably and does 10s of thousands of alignments a month...



On 16/03/2018 12:58, Héctor Montero wrote:
Thanks for the answer. I tried too many times already so I did the alignment in MUSCLE webpage instead and now all I want to do is to visualize an alignment already done in MUSCLE in Jalview. Can you advise me how to do it?.
Thanks
Hector

On Fri, Mar 16, 2018 at 12:12 PM, Geoff Barton <***@dundee.ac.uk<mailto:***@dundee.ac.uk>> wrote:

Dear Héctor,

Sorry you have been having problems doing alignments in Jalview. I've just tried it, it was slow, but did come back with an alignment.

There were some problems with our cluster over the last few days which may have caused what you are seeing. Please try again and ideally post your experience on the jalview-discuss mailing list.

Incidentally, were you aware that you can do the alignments locally by installing JABAWS? For instructions, please see: www.compbio.dundee.ac.uk/jabaws<http://www.compbio.dundee.ac.uk/jabaws>.

With thanks,

Geoff.


On 16/03/2018 11:52, Héctor Montero wrote:
Hello, I want to align 37 sequences (input by plain text) in Jalview using the function Muscle by default. When I do this, the job appears a queuing endlessly and after a while, an error message appears. This does not happen when I input a few sequences. So I want to ask you how can I instead input an alignment already performed in Muscle into Jalview. Apparently I cannot just copy and paste the results I got in Muscle because they are not continuous.
Thanks
Hector

--
Héctor Montero Sommerfeld



--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | ***@dundee.ac.uk<mailto:***@dundee.ac.uk>
Tel: [phone]<tel:+44%201382%20385860> | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton


The University of Dundee is registered Scottish charity: No.SC015096


The University of Dundee is a registered Scottish Charity, No: SC015096



--
Héctor Montero Sommerfeld



--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | ***@dundee.ac.uk<mailto:***@dundee.ac.uk>
Tel: [phone] | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton


The University of Dundee is registered Scottish charity: No.SC015096


The University of Dundee is a registered Scottish Charity, No: SC015096

[Geoff Barton]

A brief update:

The alignment running problems with Jalview are now fixed.

If anyone reading this ever has a problem with any of the Jalview webservices, please do let us know. We do have automatic testing of the services but sometimes error conditions happen that are not identified by these tests.

Thanks again,

Geoff.

On 16/03/2018 12:12, Geoff Barton wrote:

Dear Héctor,

Sorry you have been having problems doing alignments in Jalview. I've just tried it, it was slow, but did come back with an alignment.

There were some problems with our cluster over the last few days which may have caused what you are seeing. Please try again and ideally post your experience on the jalview-discuss mailing list.

Incidentally, were you aware that you can do the alignments locally by installing JABAWS? For instructions, please see: www.compbio.dundee.ac.uk/jabaws<http://www.compbio.dundee.ac.uk/jabaws>.

With thanks,

Geoff.

On 16/03/2018 11:52, Héctor Montero wrote:
Hello, I want to align 37 sequences (input by plain text) in Jalview using the function Muscle by default. When I do this, the job appears a queuing endlessly and after a while, an error message appears. This does not happen when I input a few sequences. So I want to ask you how can I instead input an alignment already performed in Muscle into Jalview. Apparently I cannot just copy and paste the results I got in Muscle because they are not continuous.
Thanks
Hector

--
Héctor Montero Sommerfeld



--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | ***@dundee.ac.uk<mailto:***@dundee.ac.uk>
Tel: [phone] | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton


The University of Dundee is registered Scottish charity: No.SC015096


The University of Dundee is a registered Scottish Charity, No: SC015096


_______________________________________________
Jalview-discuss mailing list
Jalview-***@jalview.org<mailto:Jalview-***@jalview.org>
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss



--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology
School of Life Sciences | University of Dundee, Scotland, UK | ***@dundee.ac.uk<mailto:***@dundee.ac.uk>
Tel: [phone] | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton


The University of Dundee is registered Scottish charity: No.SC015096


The University of Dundee is a registered Scottish Charity, No: SC015096