MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0001059MEGAAlignment Explorerpublic2019-01-04 05:092019-01-11 21:39
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionfixed 
PlatformPCOSWindowsOS Version7
Product Version 
Target VersionFixed in Version 
First NameJanos
Last NameAgoston
Emailagoston.janos123@gmail.com
Confirm Emailagoston.janos123@gmail.com
Summary0001059: Clustal alignment import problem
DescriptionDear Address,
I have came across a bug. I imported Clustal alignment to MegaX, and when I clicked Phylogenetic Analysis an error meggage came up. It seems, that when I import amino acid alignment with conserved sites the stars and points are imported as a last sequence. When I delete the wrongly imported last line it works well.
Here is a video I just made from the bug: https://youtu.be/1yQsH7u7SDQ [^]
Regards,
Janos
Steps To Reproduceimport an amino acid Clustal alignment from a file (preferably with lots of conserved amino acids) and hit Phylogenetic Analysis
Additional InformationI have not tested this with nucleotides.
TagsNo tags attached.
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Issue History
Date ModifiedUsernameFieldChange
2019-01-04 05:09guestNew Issue
2019-01-07 07:35gstecherNote Deleted: 0001035
2019-01-07 07:48gstecherAssigned To => gstecher
2019-01-07 07:48gstecherStatusnew => assigned
2019-01-07 07:48gstecherNote Added: 0004160
2019-01-08 09:37gstecherNote Added: 0004176
2019-01-11 21:39gstecherNote Added: 0004180
2019-01-11 21:39gstecherStatusassigned => resolved
2019-01-11 21:39gstecherResolutionopen => fixed

Notes
(0004160)
gstecher   
2019-01-07 07:48   
Hi Janos,

I am writing in response to the bug report you recently submitted regarding the MEGA software. Can you send me the .aln file you used when you encountered the problem with importing a Clustal alignment. That would help me investigate the problem. Thanks!

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu
(0004176)
gstecher   
2019-01-08 09:37   
Hi Janos,

Thanks for sending that file. It looks like the error is caused because MEGA does not recognize that the last line in the .aln file is not sequence data but rather describes the level of conservation at each site. This will be fixed in the next release of MEGA. Until then, the workaround is to delete the last row in the Alignment Explorer or open the .aln files in a text editor and delete the last row in the file.
On 1/8/2019 7:53 AM, J. Agoston wrote:
> Dear Glen,
>
> Thank you for your reply! I'm sending you the alignment file in attachment.
> Regards,
> Janos
(0004180)
gstecher   
2019-01-11 21:39   
fixed by Christina in 10.1.0