0001938: degenerate nucleotides - MantisBT

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ID

Project

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Date Submitted

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0001938

MEGA

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public

2020-04-22 07:27

2020-05-07 10:42

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

0001938: degenerate nucleotides

Description

I've been trying to figure out how Mega deals with sequences which have degenerate bases (W,S,M,R,Y,etc) when it calculates alignments using Muscle and when it actually does phylogeny using neighbor joining. But I have been unable to locate this information. Can you help?

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First Name

charlotte

Last Name

stanley

Email

charlotte.blowe@goldsboromilling.com

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charlotte.blowe@goldsboromilling.com

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Notes
(0004459) gstecher (administrator) 2020-05-07 10:42	Hi Charlotte, I am writing in response to your question regarding the MEGA software. For the neighbor-joining method in MEGA, degenerate bases are treated as ambiguous data. As far as how MUSCLE treats degenerate bases you can search the MUSCLE documentation at https://drive5.com/muscle/manual/ [^] -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

(0004460) gstecher (administrator) 2020-05-07 10:42	Hi Charlotte, I am writing in response to your question regarding the MEGA software. For the neighbor-joining method in MEGA, degenerate bases are treated as ambiguous data. As far as how MUSCLE treats degenerate bases you can search the MUSCLE documentation at https://drive5.com/muscle/manual/ [^] -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

Issue History
Date Modified	Username	Field	Change
1969-12-31 17:33	agasky	Status	new => assigned
1969-12-31 17:33	agasky	Assigned To	=> agasky
1969-12-31 17:33	user614	Assigned To	agasky => user614
1969-12-31 17:33	user614	Note Added: 0001912
1969-12-31 17:33	user614	Note Added: 0001913
1969-12-31 17:33	user614	Status	assigned => closed
1969-12-31 17:33	user614	Resolution	open => won't fix
2020-04-22 07:27	guest	New Issue
2020-04-27 07:33	gstecher	File Deleted: gggg.tif
2020-05-07 10:41	gstecher	Note Deleted: 0001912
2020-05-07 10:41	gstecher	Note Deleted: 0001913
2020-05-07 10:42	gstecher	Note Added: 0004459
2020-05-07 10:42	gstecher	Note Added: 0004460
2020-05-07 10:42	gstecher	Status	new => resolved
2020-05-07 10:42	gstecher	Resolution	open => no change required
2020-05-07 10:42	gstecher	Assigned To	=> gstecher

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