MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0001938MEGA[All Projects] Feedbackpublic2020-04-22 07:272020-05-07 10:42
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product Version 
Target VersionFixed in Version 
First Namecharlotte
Last Namestanley
Emailcharlotte.blowe@goldsboromilling.com
Confirm Emailcharlotte.blowe@goldsboromilling.com
Summary0001938: degenerate nucleotides
DescriptionI've been trying to figure out how Mega deals with sequences which have degenerate bases (W,S,M,R,Y,etc) when it calculates alignments using Muscle and when it actually does phylogeny using neighbor joining. But I have been unable to locate this information. Can you help?
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Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33agaskyStatusnew => assigned
1969-12-31 17:33agaskyAssigned To => agasky
1969-12-31 17:33user614Assigned Toagasky => user614
1969-12-31 17:33user614Note Added: 0001912
1969-12-31 17:33user614Note Added: 0001913
1969-12-31 17:33user614Statusassigned => closed
1969-12-31 17:33user614Resolutionopen => won't fix
2020-04-22 07:27guestNew Issue
2020-04-27 07:33gstecherFile Deleted: gggg.tif
2020-05-07 10:41gstecherNote Deleted: 0001912
2020-05-07 10:41gstecherNote Deleted: 0001913
2020-05-07 10:42gstecherNote Added: 0004459
2020-05-07 10:42gstecherNote Added: 0004460
2020-05-07 10:42gstecherStatusnew => resolved
2020-05-07 10:42gstecherResolutionopen => no change required
2020-05-07 10:42gstecherAssigned To => gstecher

Notes
(0004459)
gstecher   
2020-05-07 10:42   
Hi Charlotte,

I am writing in response to your question regarding the MEGA software. For the neighbor-joining method in MEGA, degenerate bases are treated as ambiguous data. As far as how MUSCLE treats degenerate bases you can search the MUSCLE documentation at https://drive5.com/muscle/manual/ [^]

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu
(0004460)
gstecher   
2020-05-07 10:42   
Hi Charlotte,

I am writing in response to your question regarding the MEGA software. For the neighbor-joining method in MEGA, degenerate bases are treated as ambiguous data. As far as how MUSCLE treats degenerate bases you can search the MUSCLE documentation at https://drive5.com/muscle/manual/ [^]

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu