MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0000347MEGA[All Projects] Feedbackpublic2016-12-20 17:042016-12-22 15:08
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameNitish
Last NameNarula
Emailnitish.narula@outlook.com
Confirm Emailnitish.narula@outlook.com
Summary0000347: Reltime multi-species outgroup clade
DescriptionHi,

Firstly, I cannot find a user forum to ask this question nor does the documentation clarify this. If there is a user forum, please let me know.

I would like to set a clade of three species as outgroup in the groups file. I tried putting all three, one per line, like so:
speciesA=outgroup
speciesB=outgroup
speciesC=outgroup

But the results show the clade with zero branchlengths. What am I doing wrong? Any help appreciated.

Thank you,
Nitish
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Issue History
Date ModifiedUsernameFieldChange
2016-12-20 17:04guestNew Issue
2016-12-22 15:08gstecherNote Added: 0003730
2016-12-22 15:08gstecherStatusnew => resolved
2016-12-22 15:08gstecherResolutionopen => no change required
2016-12-22 15:08gstecherAssigned To => gstecher

Notes
(0000241)
gstecher   
1969-12-31 17:33   
I need to add a redirect to the MEGA website so users don\'t get confused by the 404 error message.
(0000263)
gstecher   
1969-12-31 17:33   
Our Westhost account is currently screwed up so I cant get the access I need to fix this. I\'ll fix it when access is restored.
(0000266)
gstecher   
1969-12-31 17:33   
Fixed.
(0003730)
gstecher   
2016-12-22 15:08   
Hi Nitish,

I am writing in response to your question regarding the Reltime analysis in MEGA. You are not doing anything wrong. By default, MEGA compresses the outgroup for the Reltime analysis. According to the appnote paper describing the release of MEGA7:

"It is important to note that MEGA7 does not use calibrations that are present in the clade containing the outgroup(s), because that would require an assumption of equal rates of evolution between the ingroup and outgroup sequences, which cannot be tested. For this reason, timetrees displayed in the Tree Explorer have the outgroup cluster compressed and grayed out by default to promote correct scientific analysis and interpretation."

If you are using the GUI version of MEGA, you can uncompress the outgroup using the formatting tools on the left toolbar.

--
Best regards,

Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu