MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0001254MEGA[All Projects] Feedbackpublic2019-05-31 06:412023-04-14 18:41
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusassignedResolutionopen 
PlatformOSOS Version
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameJacob
Last NameRoved
Emailjacob.roved@biol.lu.se
Confirm Emailjacob.roved@biol.lu.se
Summary0001254: Bug in p-distance calculation?
DescriptionI've been using MEGA 6 for P-distance calculations, but discovered what I believe is a bug. When I open a nucleotide sequence alignment and calculate P-distances based on amino acids, I do not get the same values as when I manually translate my nucl. sequences to amino acid sequences and calculate P-distances based on that alignment. This is unexpected. Can you please provide an explanation to why this is, and what is actually calculated when a nucleotide alignment is used as input. Thank you.
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Issue History
Date ModifiedUsernameFieldChange
2019-05-31 06:41guestNew Issue
2019-05-31 12:42gstecherAssigned To => gstecher
2019-05-31 12:42gstecherStatusnew => assigned
2019-05-31 12:43gstecherNote Added: 0004253
2022-03-08 07:40guestNote Added: 0005038
2022-12-05 06:43guestNote Added: 0005809
2023-04-14 18:41guestNote Added: 0006529

Notes
(0004253)
gstecher   
2019-05-31 12:43   
Hi Jacob,

I am writing in response to your question regarding the MEGA 6 software. I am not able to duplicate the bug you reported. Please double check what you are doing and make sure you use the same code table and codon start for each case. If there is still a difference, please send me the nucleotide alignment and I will have a look.

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu
(0005038)
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2022-03-08 07:40   
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(0005809)
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(0006529)
guest   
2023-04-14 18:41   
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