MantisBT - MEGA
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IDProjectCategoryView StatusDate SubmittedLast Update
0006633MEGATimetree Wizardpublic2024-12-13 02:492024-12-13 02:49
Reporterguest 
Assigned To 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusnewResolutionopen 
PlatformPCOSLinuxOS Versionother
Product VersionMEGA-CC 11 (command line version) 
Target VersionFixed in Version 
First NameGontran
Last NameSonet
Emailgsonet@naturalsciences.be
Confirm Emailgsonet@naturalsciences.be
Summary0006633: Output of RelTime not providing node ages
DescriptionDear 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 ReproduceCommand 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 Informationsee 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!
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Attached Filestxt M11CC_AllUCE-Cal_summary.txt (4,247) 2024-12-13 02:49
https://megasoftware.net/mantis_bt/
? M11CC_AllUCE-Cal_exactTimes.nwk (3,396) 2024-12-13 02:49
https://megasoftware.net/mantis_bt/
Issue History
Date ModifiedUsernameFieldChange
2024-12-13 02:49guestNew Issue
2024-12-13 02:49guestFile Added: M11CC_AllUCE-Cal_summary.txt
2024-12-13 02:49guestFile Added: M11CC_AllUCE-Cal_exactTimes.nwk

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