MantisBT - MEGA
View Issue Details
IDProjectCategoryView StatusDate SubmittedLast Update
0001926MEGA[All Projects] Feedbackpublic2020-04-17 02:592020-05-08 07:40
Reporterguest 
Assigned Togstecher 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusresolvedResolutionno change required 
PlatformOSOS Version
Product Version 
Target VersionFixed in Version 
First NameAmaya
Last NameVelasco
Emailamayavelasco@iim.csic.es
Confirm Emailamayavelasco@iim.csic.es
Summary0001926: Phylogenetic model
DescriptionGood morning.
We have been using Tamura-Nei model for the NJ tree for species identification, but now we are trying to separate very closely related species, and I would like to know if there is a model o a parameter that we can use in order to give more importance certain SNPs than others.
Thank you
Steps To Reproduce
Additional Information
TagsNo tags attached.
Relationships
Attached Files
Issue History
Date ModifiedUsernameFieldChange
1969-12-31 17:33agaskyNote Added: 0001690
1969-12-31 17:33agaskyStatusnew => closed
1969-12-31 17:33agaskyResolutionopen => fixed
2020-04-17 02:59guestNew Issue
2020-05-07 10:46gstecherNote Added: 0004461
2020-05-07 10:46gstecherStatusnew => resolved
2020-05-07 10:46gstecherResolutionopen => no change required
2020-05-07 10:46gstecherAssigned To => gstecher
2020-05-07 10:46gstecherNote Deleted: 0001690
2020-05-08 07:40gstecherNote Added: 0004462

Notes
(0004461)
gstecher   
2020-05-07 10:46   
Hi Amaya,

I am writing in response to your question regarding the MEGA software. Thanks for your question but no, MEGA does not provide a way to give weights to different SNPs. I am curious though. Have you seen this capability in other software or seen any publications describing such a method?

--
Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu
(0004462)
gstecher   
2020-05-08 07:40   
Dear Glen,

Thank you for your response. No, we didn't find anything like this in any publication, but the need arose in order to diffrentiate very similar species: we know that some SNPs are informative and others are not, and we wanted to know if there is way to reflect that in a phylogenetic tree.

Thanks again,

Amaya