MantisBT - MEGA
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0004294MEGA[All Projects] Feedbackpublic2022-12-28 00:412023-04-14 00:51
guest 
 
normalminorhave not tried
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MEGA 11 (Graphical Interface version) 
 
David
Bahry
davidbahry@cmail.carleton.ca
davidbahry@cmail.carleton.ca
0004294: test for selection: caption + walkthrough
Hello! For the Z-test for selection,

- The caption calls Prob "The probability of rejecting the null hypothesis of strict-neutrality (dN = dS) in favor of the alternative hypothesis." That's backwards; e.g. Prob=1 means the null *does* perfectly fit the data. It should just say "The p-value," or else accurately describe the p-value.

- "Drosophila_Adh.meg" may be better than "HLA-3Seq.meg" for the walkthrough (or include both), since the test does detect selection in Adh, but not in HLA-3.
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Issue History
1969-12-31 17:33user614Note Added: 0002961
1969-12-31 17:33user614Note Added: 0002964
1969-12-31 17:33user614Note Added: 0002965
1969-12-31 17:33user614Note Added: 0002966
1969-12-31 17:33user614Note Added: 0002967
1969-12-31 17:33user19Statusnew => assigned
1969-12-31 17:33user19Assigned To => user614
1969-12-31 17:33user614Note Added: 0002970
1969-12-31 17:33user614Statusassigned => closed
1969-12-31 17:33user614Resolutionopen => won't fix
2022-12-28 00:41guestNew Issue
2023-04-14 00:51guestNote Added: 0006343

Notes
(0002961)
user614   
1969-12-31 17:33   
Hello Henry,

I am writing in response to the bug report you recently submitted regarding the model selection analysis in MEGA. When you run the analysis, the Caption Expert should be displayed with the results in a table. Does the Caption Expert window appear after the analysis completes? If so, are you able to export the results by clicking on either the Excel or CSV export buttons?

Best regards,

Glen Stecher
(0002964)
user614   
1969-12-31 17:33   
Hi Glen,
 
Thanks for the quick response.
 
No, the Caption Expert window for the results does not appear at all, so there is no way to try to export the results.
 
I even did a different, prior analysis (e.g., substitution matrix) and have its results displayed in an Caption Expert window and kept open, to check that all is fine during the model selection (e.g., that the Caption Expert routines are still up and running).
 
My speculation is that some function call to display the results got mislaid...
(0002965)
user614   
1969-12-31 17:33   
Hi Henry,
 
  Can you tell me which version of MEGA you are using (the current version is 5.10) as well as which operating system you are using? If you are not using version 5.10 then upgrading may fix the problem. I can send you a download link for the most current version if needed, just let me know which os you have. Also, when you run the model selection analysis, is a progress dialog displayed? If it is displayed, does it run to 100%?
 
Best regards,
 
Glen Stecher
(0002966)
user614   
1969-12-31 17:33   
Hi Glen,

I was using the 5.10 version, running under XP-like environment (Crossover 12.1.1 WINE).

As far as I can tell, the model selection did run thru a number of models, although I don't know if it went thru all of them.

Were you able to reproduce the phenomenon?
(0002967)
user614   
1969-12-31 17:33   
Hi Henry,

Yes, I am able to duplicate the bug when running MEGA using Wine. However, I suspect that this is not really a bug in MEGA but rather a consequence of running under Wine, which often requires some customization/configuration. I will fiddle around with the Wine debugger and see if I can quickly identify the problem but if not, we unfortunately won’t be able to provide a fix. However, the CodeWeavers has several support options that may be helpful.

Best regards,

Glen Stecher
(0002970)
user614   
1969-12-31 17:33   
The problem does not exist in the Windows or Mac versions so we won't fix this now as Linux is not supported.
(0006343)
guest   
2023-04-14 00:51   
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