MantisBT - MEGA
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0000490MEGA[All Projects] Feedbackpublic2017-07-04 07:372017-07-13 09:18
guest 
gstecher 
normalminorhave not tried
resolvedwon't fix 
MEGA 11 (Graphical Interface version) 
 
Robert
Goldberg-Alberts
alberts-3@comcast.net
alberts-3@comcast.net
0000490: Newick Format Error
When using "Clocks" tool, I get the following error: "Oh no! An error has occurred:Failed to parse Newick file."

Am I doing something wrong (most likely) or is there a fix? I am using Version 6 on Windows per class assignment. I would be grateful if you could advise.

Mega is a wonderful tool and I am enjoying the learning experience! Congratulations on a job well done!
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Issue History
2017-07-04 07:37guestNew Issue
2017-07-10 12:22gstecherAssigned To => gstecher
2017-07-10 12:22gstecherStatusnew => assigned
2017-07-10 12:22gstecherNote Added: 0003823
2017-07-13 09:18gstecherNote Added: 0003829
2017-07-13 09:18gstecherStatusassigned => resolved
2017-07-13 09:18gstecherResolutionopen => won't fix

Notes
(0000497)
paul   
1969-12-31 17:33   
Thanks you notes has been sent and suggestion is saved. This bug is closed.
(0003823)
gstecher   
2017-07-10 12:22   
Hi Robert,

I am writing in response to the bug report you recently submitted regarding the MEGA software. Can you send me the data files you were using when you encountered the error so that I can duplicate the issue?

--
Best regards,

Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu
(0003829)
gstecher   
2017-07-13 09:18   
Hi Robert,

Thanks for sending those files. It looks like MEGA6 has problems with the double underscore characters that are in the taxa names. In the attached files I have replaced the double underscores with single underscores and now it is working. For information about the bioinformatics community at Temple have a look at http://igem.temple.edu/ [^]

On 7/12/2017 3:45 AM, Amy and Robert Alberts wrote:
> Glen: Thank you for responding. I have included the files above. Some background: I am taking a course on Coursera.org in Bioinformatics. The sponsoring organization is the University of California at San Diego. In one of the classes they use MEGA. One other student has reported this error. I was using MEGA6 at the time. I also downloaded MEGA7; however, the class uses version 6 so to reproduce the answers the project is looking for I have to use version 6. Presumably the defaults for major programs are different between the two versions.
>
> I am a tyro at using MEGA. I used it briefly in one of my previous courses on Coursera from the University of Toronto. So this might be my mistake.
>
> Hope this helps. I see you are at Temple. Is there a Bioinformatics community at Temple? I live in Philadelphia and would be interested in knowing.
>
> Thanks again for responding.
>
> Robert