MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0003725MEGA[All Projects] Feedbackpublic2022-06-01 00:522022-06-08 07:57
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product Version 
Target VersionFixed in Version 
First NameBryan
Last NameSubong
Emailbjsubong@chem.s.u-tokyo.ac.jp
Confirm Emailbjsubong@chem.s.u-tokyo.ac.jp
Summary0003725: regarding error J amino acid
DescriptionHi MEGA!

I am encountering a problem. A aligned my protein pop gen data in Geneious software and got the haplotypes. When I exported it to MEGA, MEGA says there is an invalid element- J amino acid. However, this does not appear in any of my sequences using other programs or if I use the MEGA text editor.

What is the reason for this problem and how can I address this? Thanks
Steps To Reproduce
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Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33user614Tag Attached: image_export
1969-12-31 17:33user614Note Added: 0002586
1969-12-31 17:33user614CategoryTree Explorer => Image Export
1969-12-31 17:33user614Product Version5.0 =>
2022-06-01 00:52guestNew Issue
2022-06-08 07:57gstecherNote Added: 0005630
2022-06-08 07:57gstecherStatusnew => resolved
2022-06-08 07:57gstecherResolutionopen => no change required
2022-06-08 07:57gstecherAssigned To => gstecher

Notes
(0002586)
user614   
1969-12-31 17:33   
We should really try to improve this but it is not a high priority. However, maybe we can take a quick look at the code and make sure that there isn't some obvious way to make this more efficient.
(0005630)
gstecher   
2022-06-08 07:57   
Hi Bryan,

Thanks for sending those files. MEGA does not support the ambiguous J symbol for leucine or isoleucine so you may need to replace those symbols with the ? symbol for missing data to analyze your data in MEGA. Regarding the second error, there are sequences of differing lengths and it seems the sequences have not been aligned. Below is a screen shot of the first file where a couple of sequences are shorter than the others.