MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0001235MEGA[All Projects] Feedbackpublic2019-05-15 17:462019-05-23 15:10
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product VersionMEGA Website 
Target VersionFixed in Version 
First NameSupriyo
Last NameBasak
Emailbasak@mail.kib.ac.cn
Confirm Emailbasak@mail.kib.ac.cn
Summary0001235: request to solve error message for constucting time calibrated phylogenetic tree in MEGA
DescriptionRespected Prof. Dr. Tamura, Stecher, Peterson, Filipski, and Kumar,

Following your example, I have created my own newick file (in mega) for constructing the time calibrated phylogenetic tree. After that I am getting error message

"Failed to parse newick file" (I have attached the error message for your kind perusal in a powerpoint). Please help me to solve my problem
Thanks
Supriyo Basak
Kunming Institute of Botany




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Issue History
Date ModifiedUsernameFieldChange
2019-05-15 17:46guestNew Issue
2019-05-16 14:38gstecherAssigned To => gstecher
2019-05-16 14:38gstecherStatusnew => assigned
2019-05-16 14:38gstecherNote Added: 0004248
2019-05-23 15:10gstecherNote Added: 0004251
2019-05-23 15:10gstecherStatusassigned => resolved
2019-05-23 15:10gstecherResolutionopen => no change required

Notes
(0004248)
gstecher   
2019-05-16 14:38   
Hi Supriyo,

I am writing in response to your question regarding the MEGA software. Can you send me the newick file that MEGA fails to parse so I can have a look?

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu
(0004251)
gstecher   
2019-05-23 15:10   
Hi Supriyo,

Relative times have no unit. You can think of them more like ratios as they inform us about the relative distance between divergence times throughout the tree. To get divergence times you need to provide at least one calibration constraint. In the example data provided with MEGA, the mtCDNA files are for a tree of great apes and we provide a constraint that bonobo and chimpanzee diverged from a common ancestor between 2.4 and 3.2 million years ago. MEGA uses this to convert all relative times in the tree to real times of divergence.
On 5/20/19 8:59 PM, Supriyo Basak wrote:
>
> Dear Dr. Glen Stecher,
>
> Many many thanks for clarifying the outgruop. I am seeing the papers which have been published citing timetree analysis using RelTime method have given the axis bar on milions year ago. But the attached tree is the on replative time units. Could you kindly let me know that 0.01 relative time corrosponds to how many milions years. I am not gettig how to correlate this two paramenters.
>
> Yours sincerely
>
> Supriyo Basak
>
> Post Doc, Kunming Institute of Botany
>
> Timetree analysis using the RelTime method on matK locus