MantisBT - MEGA
View Issue Details
IDProjectCategoryView StatusDate SubmittedLast Update
0002083MEGA[All Projects] Feedbackpublic2020-06-19 10:502020-06-19 14:44
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionwon't fix 
PlatformOSOS Version
Product VersionMEGA 11 (Graphical Interface version) 
Target VersionFixed in Version 
First NameSOUMILA
Last NameMONDAL
Emailsoumila.bhu@gmail.com
Confirm Emailsoumila.bhu@gmail.com
Summary0002083: Problem regarding ML tree building
DescriptionHello Sir/Madam,
I Soumila Mondal, a research scholar from Banaras Hindu University is writing to you as I am facing difficulties during tree building. Currently, I am working on a protein that bears selenocysteine (U). During ML tree construction the software pop up a window having a message unusual amino acid residue found. The residue U is so important for my study thus I can't delete it. Thus I request you to give me suggestions on this matter as soon as possible.
Thanking You
Steps To Reproduce
Additional Information
TagsNo tags attached.
Relationships
Attached Files
Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33user19Statusnew => closed
1969-12-31 17:33user19Resolutionopen => fixed
2020-06-19 10:50guestNew Issue
2020-06-19 14:44gstecherNote Added: 0004482
2020-06-19 14:44gstecherStatusnew => resolved
2020-06-19 14:44gstecherResolutionopen => won't fix
2020-06-19 14:44gstecherAssigned To => gstecher

Notes
(0004482)
gstecher   
2020-06-19 14:44   
Hi Soumila,

I am writing in response to your question regarding the MEGA software. Unfortunately the models used in MEGA do not support selenocysteine so the only option for analyzing the data in MEGA would be to treat those bases as ambiguous data. I think you might want to look at RAxML, Phyml, PAML, or some other software for constructing an ML tree and see if any of them support selenocysteine.

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