0001926: Phylogenetic model - MantisBT

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ID

Project

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Date Submitted

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0001926

MEGA

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public

2020-04-17 02:59

2020-05-08 07:40

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

no change required

Platform

OS

Product Version

Target Version

Fixed in Version

Summary

0001926: Phylogenetic model

Description

Good 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

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First Name

Amaya

Last Name

Velasco

Email

amayavelasco@iim.csic.es

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amayavelasco@iim.csic.es

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Notes
(0004461) gstecher (administrator) 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 (administrator) 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

Issue History
Date Modified	Username	Field	Change
1969-12-31 17:33	agasky	Note Added: 0001690
1969-12-31 17:33	agasky	Status	new => closed
1969-12-31 17:33	agasky	Resolution	open => fixed
2020-04-17 02:59	guest	New Issue
2020-05-07 10:46	gstecher	Note Added: 0004461
2020-05-07 10:46	gstecher	Status	new => resolved
2020-05-07 10:46	gstecher	Resolution	open => no change required
2020-05-07 10:46	gstecher	Assigned To	=> gstecher
2020-05-07 10:46	gstecher	Note Deleted: 0001690
2020-05-08 07:40	gstecher	Note Added: 0004462

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