Alignments

geoff.barton · 16 March 2018 12:12

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.

With thanks,

Geoff.

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

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

···

On 16/03/2018 11:52, Héctor Montero wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

geoff.barton · 16 March 2018 13:13

Hi Héctor,

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

https://www.youtube.com/watch?v=AJGQJQtGs-Q&t=2s

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…

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
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.

With thanks,

Geoff.

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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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

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

···

On 16/03/2018 12:58, Héctor Montero wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

geoff.barton · 16 March 2018 15:23

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.

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.

With thanks,

Geoff.

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

The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)

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

···

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

On 16/03/2018 11:52, Héctor Montero wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

geoff.barton · 18 August 2019 17:26

Hello Geoff, what is the next step after downloading the installer. I ended up with Install4j in my computer with no clue what to do next.
Thanks
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.
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.

With thanks,

Geoff.

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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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

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

···

On 18/08/2019 17:15, Héctor Montero wrote:

-- 
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

geoff.barton · 18 August 2019 17:28

Hi Héctor,

You are trying to install Version 2.11? Which operating system are you using? Windows/mac/Linux?

Geoff.

Sorry for multiple mails - I wanted to reply to the list but messed it up. Geoff.

Hello Geoff, what is the next step after downloading the installer. I ended up with Install4j in my computer with no clue what to do next.
Thanks
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.
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.

With thanks,

Geoff.

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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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
The University of Dundee is a registered Scottish Charity, No: SC015096

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

···

On 18/08/2019 18:26, Geoff Barton wrote:

On 18/08/2019 17:15, Héctor Montero wrote:

-- 
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)

-- 
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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

geoff.barton · 18 August 2019 20:45

Did you do the following on Windows?

click the big green arrow that is in the top right of the www.jalview.org page
download and save the installation file for windows
double click the file and follow the instructions - most people can just click OK to everything.

This should work OK and end up with you having a Jalview icon on the desktop. When you click on this icon it starts Jalview.

I just tried it on an old Windows 8 installation and it worked. Ben Soares who developed the new installer and others in the group here have tested it on several versions of winows up to and including Windows 10.

If you are still having problems, please let us know (1) which version of Windows you are running on and (2) exactly the steps you followed.

With thanks,

Geoff.

P.S. I have copied this reply to jalview-discuss since others may also be having problems installing on windows. We know many people are successfully using 2.11 on windows so your problems might be very specific to a particular version of windows or to the steps you followed.

Yes, I want to install version 2.11 in windows
Hi Héctor,

You are trying to install Version 2.11? Which operating system are you using? Windows/mac/Linux?

Geoff.

Sorry for multiple mails - I wanted to reply to the list but messed it up. Geoff.
Hello Geoff, what is the next step after downloading the installer. I ended up with Install4j in my computer with no clue what to do next.
Thanks
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.
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.

With thanks,

Geoff.

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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](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 | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
-- 
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [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

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

···

On 18/08/2019 19:08, Héctor Montero wrote:

-- 
Geoff Barton, FRSE FRSB | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

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