0002672: branch lenghts on ML tree

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Date Submitted

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0002672

MEGA

Suggestion

public

2021-03-25 19:38

2021-03-26 10:36

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

no change required

Platform

Linux

Product Version

MEGA-CC 11 (command line version)

Target Version

Fixed in Version

Summary

0002672: branch lenghts on ML tree

Description

I've run a Maximum likelihood analysis using Bootstrap for testing the tree. However in Tree Explorer I only can visualize bootstraps values on a ultrametric tree. I would like to see them on the branches of the original tree.
I am using Mega X:

Steps To Reproduce

Evolutionary analysis by Maximum Likelihood method
The evolutionary history was inferred by using the Maximum Likelihood method and Hasegawa-Kishino-Yano model [1]. The bootstrap consensus tree inferred from 500 replicates [3] is taken to represent the evolutionary history of the taxa analyzed [3]. Branches corresponding to partitions reproduced in less than 50% bootstrap replicates are collapsed. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches [3]. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. This analysis involved 43 nucleotide sequences. There were a total of 4711 positions in the final dataset. Evolutionary analyses were conducted in MEGA X [2]

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First Name

Fernanda

Last Name

Antunes Carvalho

antunesfc@gmail.com

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antunesfc@gmail.com

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Notes
(0002082) user19 1969-12-31 17:33	fixed bug in commit #7 (98a30855dc13) refer to SVN for details on bug fix.

(0004565) gstecher (administrator) 2021-03-26 10:36	Hi Fernanda, I am writing in response to your question regarding bootstrap values in MEGA. To view them on the original tree in the Tree Explorer, select the Original Tree tab, then click View->Show/Hide->Stats/Frequency. 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	user19	Note Added: 0002082
1969-12-31 17:33	user19	Status	new => resolved
1969-12-31 17:33	user19	Resolution	open => fixed
1969-12-31 17:33	user19	Assigned To	=> user19
2021-03-25 19:38	guest	New Issue
2021-03-26 10:36	gstecher	Note Added: 0004565
2021-03-26 10:36	gstecher	Status	new => resolved
2021-03-26 10:36	gstecher	Resolution	open => no change required
2021-03-26 10:36	gstecher	Assigned To	=> gstecher