MantisBT - MEGA |
| View Issue Details |
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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0000704 | MEGA | Tree Explorer | public | 2018-03-21 03:10 | 2018-04-11 15:35 |
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| Reporter | guest | |
| Assigned To | gstecher | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | resolved | Resolution | unable to reproduce | |
| Platform | PC | OS | Windows | OS Version | 10 |
| Product Version | MEGA 11 (Graphical Interface version) | |
| Target Version | | Fixed in Version | | |
| First Name | Tiphaine |
| Last Name | Le Roy |
| Email | tiphaine.leroy@uclouvain.be |
| Confirm Email | tiphaine.leroy@uclouvain.be |
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| 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
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| 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. |
| Tags | No tags attached. |
| Relationships | |
| Attached Files |  analyse 16 S transmi 1.zip (38,804) 2018-03-21 03:10
https://megasoftware.net/mantis_bt/ |
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| 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 |
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Notes |
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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?
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Best regards,
Glen Stecher
Institute for Genomics and Evolutionary Medicine
igem.temple.edu |
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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 |
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