MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000338MEGACalculation Errorpublic2016-12-09 07:592023-04-14 00:51
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformOSOS Version
Product Version 
Target VersionFixed in Version 
First NameDorcas
Last NameOrengo
Emaildorcasorengo@ub.edu
Confirm Emaildorcasorengo@ub.edu
Summary0000338: synonymous nucleotide substitutions
DescriptionWith MEGA6 I have already noticed this problem. Now I am testing the last version MEGA7 and I have noticed that the problem persists. I tested the program with 2 sequences 5 codons-long, which have one change each codon (2 synonymous and 3 non-synonymous). Nevertheless, I only obtain values for the non-synonymous substitutions. For the synonymous, I only obtain a red highlighted n/c, even for the number of differences!!
Steps To Reproducesequences used:
>seqA
TTTAATTTTAATAAT
>seqB
TTCAAATTCAAAAAC

Nei-Gojobori method (Number of differences)
Synonymous n/c (when actually there are 3)
Non-Synonymous 2
Additional Information
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Issue History
Date ModifiedUsernameFieldChange
2016-12-09 07:59guestNew Issue
2016-12-09 13:21gstecherFile Deleted: BwSC-3-10pct.zip
2023-01-01 16:31guestNote Added: 0005947
2023-01-01 16:47guestNote Added: 0005948
2023-01-01 18:12guestNote Added: 0005949
2023-01-01 20:40guestNote Added: 0005950
2023-01-01 21:34guestNote Added: 0005951
2023-01-02 00:24guestNote Added: 0005952
2023-01-02 03:09guestNote Added: 0005953
2023-01-02 04:21guestNote Added: 0005954
2023-01-02 04:21guestNote Added: 0005955
2023-04-14 00:51guestNote Added: 0006338

Notes
(0000250)
gstecher   
1969-12-31 17:33   
I was not able to reproduce this bug. I suggested that the user download MEGA 3 again to ensure he is using the latest version.
(0000251)
Nikita Vikhrev   
1969-12-31 17:33   
He may use parsimony. Then, MEGA stops at that moment.
(0000268)
gstecher   
1969-12-31 17:33   
Ok, this happens using MP. This should be fixed with Koichiro\'s MP code update.
(0000278)
gstecher   
1969-12-31 17:33   
Yeah, this is not really a bug. He\'s just using lots of Taxa, and MEGA really doesn\'t show any progress when it\'s searching initial trees for a large number of taxa. We should probably put some sort of additional progress graphic like in WebBrowser to show that there is still activity.
(0000345)
gstecher   
1969-12-31 17:33   
This was fixed for 3.5
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