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IDProjectCategoryView StatusDate SubmittedLast Update
0002036MEGA[All Projects] Feedbackpublic2020-06-04 08:072023-04-14 18:42
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformOS 
Product VersionMEGA Website 
Target VersionFixed in Version 
Summary0002036: Tree nodes, scale and Radiation
DescriptionDear sir
After some use of MEGAX some functions vanish: radiation tree option becomes unavailable and the scale does not appear in the Tree anymore. It seems this phenomenon occurs after Maximum parsimony usage (which gives no scale and no radiation option). After that, any tree buiding model looses radiation and scale. To fix this, I have found nothing else than to uninstal MEGAX and delete all remaining MEGAX folders in every places I can find it.
Thank you for your help
Best regards
Thierry
TagsNo tags attached.
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First NameThierry
Last NameDE MEEUS
Emailthierry.demeeus@ird.fr
Confirm Emailthierry.demeeus@ird.fr
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-  Notes
(0001828)
user19
1969-12-31 17:33

 Hello Victoria,

You indicated that you are attempting to align 20 AA sequences in the Alignment Explorer but received the error message: Error #4526: Aligned sequences must be of equal lengths (in line 10).

Did you try to open a .meg file for alignment? Could you send me the file you attempted to open which gave you the error message?

Lastly could you send me the file which you got out from ClustalW2 in meg format?

Daniel Peterson
MEGA Application Developer
Center for Evolutionary Medicine and Informatics
The Biodesign Institute @ Arizona State University
(0001832)
user19
1969-12-31 17:33

 "Smyth, Victoria" <Victoria.Smyth@afbini.gov.uk> wrote:



Hello Daniel,

Thanks for getting back to me about this. I can send you the mega files I generated using the text editor from the fasta and clustal inputs. However, the sequences I am working with are largely novel and are somewhat sensitive. Therefore before I can send them to you I have to ask you to agree to not to disclose them to anyone and that you will not keep a record of them but will delete/destroy all documents containing them as soon as you have finished working with them please?

Victoria

Dr Victoria Smyth,
Virology Dept.,
Agri-Food and Biosciences Institute,
Veterinary Sciences Division,
Stoney Road, Stormont, Belfast
Phone: 02890 525759
<Mailto:Victoria.Smyth@afbini.gov.uk<mailto:Victoria.Smyth@afbini.gov.uk>>
(0001833)
user19
1969-12-31 17:33

 From: Daniel Peterson [mailto:Daniel.E.Peterson@asu.edu]
Sent: 23 August 2010 09:32
To: Smyth, Victoria
Subject: RE: MEGA: Cannot align sequences of unequal length

That sounds fine Victoria. I will destroy the files as soon as the bug is fixed and they will never leave my computer. I will not show it to anyone else.

Daniel Peterson
(0001834)
user19
1969-12-31 17:33

 From: Smyth, Victoria [mailto:Victoria.Smyth@afbini.gov.uk]
Sent: Monday, August 23, 2010 3:07 AM
To: Daniel Peterson
Subject: RE: MEGA: Cannot align sequences of unequal length

Hi Daniel,

Attached is the meg file containing the uneven sequences I'm trying to align. I have been working on the Clustal W2 alignment since I wrote to you as I had more sequences to add and have now managed to imput it into the text editor and convert it to a meg file, from which I have constructed a tree. I would still prefer to do the alignment within mega but this seems like a way round the problem.

Victoria


Dr Victoria Smyth,
Virology Dept.,
Agri-Food and Biosciences Institute,
Veterinary Sciences Division,
Stoney Road, Stormont, Belfast
Phone: 02890 525759
<Mailto:Victoria.Smyth@afbini.gov.uk>
(0001835)
user19
1969-12-31 17:33

 Victoria,

It looks like the problem is that MEGA has some issues reading in .meg files for alignment purposes. The MEG format was designed to handle aligned sequences so for some reason the alignment explorer was expecting the sequences to be aligned (which makes no sense). I'll fix this in MEGA as soon as I can get to it. Thank you for bring this to my attention.

I noticed that the file you sent me used to be in FASTA format, is this correct? If this is, then you should know that MEGAs Alignment Explorer automatically handles reading in fasta files for alignment (no conversion necessary). For now if you can just export files in a fasta format and MEGAs alignment editor will be able to handle that. You only need meg files when you are ready to conduct an analysis (tree inference) with aligned sequences.

Did this answer the issue or have I missed something?

Dan
(0005785)
guest (reporter)
2022-12-05 06:27

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(0006550)
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2023-04-14 18:42

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- Issue History
Date Modified Username Field Change
1969-12-31 17:33 user19 Note Added: 0001828
1969-12-31 17:33 user19 Status new => acknowledged
1969-12-31 17:33 user19 Note Added: 0001832
1969-12-31 17:33 user19 Note Added: 0001833
1969-12-31 17:33 user19 Note Added: 0001834
1969-12-31 17:33 user19 Note Added: 0001835
2020-06-04 08:07 guest New Issue
2022-12-05 06:27 guest Note Added: 0005785
2023-04-14 18:42 guest Note Added: 0006550

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