0000704: Maybe a problem in exporting/importing tree with branch length in newick format

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Date Submitted

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0000704

MEGA

Tree Explorer

public

2018-03-21 03:10

2018-04-11 15:35

Reporter

guest

Assigned To

gstecher

Priority

normal

Severity

minor

Reproducibility

have not tried

Status

resolved

Resolution

unable to reproduce

Platform

Windows

Product Version

MEGA 11 (Graphical Interface version)

Target Version

Fixed in Version

Summary

0000704: Maybe a problem in exporting/importing tree with branch length in newick format

Description

I would like to generate a rooted phylogenetic tree in newick format based on my OTUs dataset in order to calculate Unifrac distance with R and Rhea scripts. For that I imported and aligned my sequences with MEGA 7, then constructed a ML tree. So far everything is perfect and easy. Then I exported the tree in Newick format with branch length. To check that everything is OK I reopened the tree with Mega 7 (user tree -> display Newick tree) and it appears that the branch length values are considered as OTU. All of this doesn't happen when I export / re open trees without branch length.

Steps To Reproduce

1 - generate the tree based on aligned sequences : open "aligned sequences" fasta file (file > open > analyze > Nucleotide sequences > non coding), then generate ML tree (phylogeny > ML tree).
2 - export the tree : file > export current tree (Newick) > branch lengths ticked > export.
3 re open the tree : user tree > display Newick tree > select the previous file

Additional Information

I'm sorry if my explanations aren't clear and/or if my problem results from an incorrect procedure. I tried to find a solution in the manual and FAQ by myself.
Except this problem I very very happy with MEGA 7 and I would like to thank you for providing at no charge this performant and user friendly software.

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First Name

Tiphaine

Last Name

Le Roy

tiphaine.leroy@uclouvain.be

Confirm Email

tiphaine.leroy@uclouvain.be

Attached Files

analyse 16 S transmi 1.zip (38,804 bytes) 2018-03-21 03:10

Relationships

Notes
(0003951) gstecher (administrator) 2018-03-27 12:35	Hi Tiphaine, I am writing in response to your recent question regarding the MEGA software. I am not able to duplicate the issue you reported. When you export to a newick file, is the newick file opened in the MEGA text editor? And does it show branch lengths? Maybe in the Tree Explorer, the View-Topology Only menu item is selected. Can you try clicking View-Topology Only? -- Best regards, Glen Stecher Institute for Genomics and Evolutionary Medicine igem.temple.edu

(0003976) gstecher (administrator) 2018-04-11 15:35	Hi Glen, Thank you very much for your answer. Yes, the Newick file is opened in the MEGA text editor and yes, the branch length are indicated. I tried clicking view-topology only but it didn't solve the problem. I manage to change my R script so that it accepted the table format and everything worked as I wanted from then, so please don't spend too much time on this problem. Best regards, tiphaine

Issue History
Date Modified	Username	Field	Change
2018-03-21 03:10	guest	New Issue
2018-03-21 03:10	guest	File Added: analyse 16 S transmi 1.zip
2018-03-27 10:13	gstecher	File Deleted: RangeCheck.jpg
2018-03-27 12:35	gstecher	Assigned To	=> gstecher
2018-03-27 12:35	gstecher	Status	new => assigned
2018-03-27 12:35	gstecher	Note Deleted: 0000659
2018-03-27 12:35	gstecher	Note Added: 0003951
2018-04-11 15:35	gstecher	Note Added: 0003976
2018-04-11 15:35	gstecher	Status	assigned => resolved
2018-04-11 15:35	gstecher	Resolution	open => unable to reproduce