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| ID | Project | Category | View Status | Date Submitted | Last Update |
| 0006633 | MEGA | Timetree Wizard | public | 2024-12-13 02:49 | 2024-12-13 02:49 |
|
| Reporter | guest | |
| Assigned To | | |
| Priority | normal | Severity | minor | Reproducibility | have not tried |
| Status | new | Resolution | open | |
| Platform | PC | OS | Linux | |
| Product Version | MEGA-CC 11 (command line version) | |
| Target Version | | Fixed in Version | | |
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| Summary | 0006633: Output of RelTime not providing node ages |
| Description | Dear Mega team,
I am using the reltime tool of MEGA on megacc.
The problem is that the output trees (.nex and .nwk) only contain info about branch lengths and not node ages. When I read Mello 2018 (Estimating TimeTrees with MEGA and the TimeTree Resource, MBE 35, 9), it seems possible to get Divergence times ("After choosing Export Current Tree (Newick), click on the TimeTree options and select Divergence Times") OR "Specifically, for timetrees, you can choose to hide the timescale and the estimated divergence times and show the estimated error bars (confidence intervals) for each node age, as well as the percentage of data coverage for each internal node (the amount of gaps/missing present while estimating a node height)". |
| Steps To Reproduce | Command line:
megacc -a reltime_ml_nucleotide75.mao -d mafft-nexus-internal-trimmed-gblocks-clean-75p-raxml.meg -t UCE75p.contree -c CalibrationFile.txt -g MEGAgroups.txt -o M11CC_AllUCE-Cal |
| Additional Information | see attached files including my output tree (.nwk) and summary (.txt)
Below my calibration file:
!MRCA=’Xylocopinae’ TaxonA='CePim2' TaxonB='XyCa 1' minTime=66.76 maxTime=92.11
!MRCA=’Anthid-Macro’ TaxonA='Ansp 1' TaxonB='MaCa 2' minTime=98.95 maxTime=123.59
...
Thank you! |
| Tags | No tags attached. |
| Attach Tags | (Separate by ",")
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|
| First Name | Gontran |
| Last Name | Sonet |
| Email | gsonet@naturalsciences.be |
| Confirm Email | gsonet@naturalsciences.be |
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| Attached Files |  M11CC_AllUCE-Cal_summary.txt (4,247 bytes) 2024-12-13 02:49
 M11CC_AllUCE-Cal_exactTimes.nwk (3,396 bytes) 2024-12-13 02:49 |
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