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TRAD
TRAD (Tip-Rooting and
Ancestor-Dating)
| Name: | TRAD |
| Main function: | As suggested by the title, used for rapidly
evolving viral strains collected over different times, without a good outgroup |
| Requirement: | (If working with a tree with >60,000 leaves): a
fast desktop computer with at least 8GB RAM |
| Keywords: | phylogenetics, dating, rooting, virus |
| Version: | 1.0.0.0 |
| Publisher: | XiaLab |
| Support: | Dr. Xuhua Xia at xxia@uottawa.ca |
| Citation: | Xia, X. 2025. TRAD: Tip-Rooting and Ancestor-Dating, version 1.2.0. https://dambe.bio.uottawa.ca/TRAD/TRAD.aspx |
 For Windows computers:
If your Windows PC already has .NET 8 installed, download and run TRADSetup.msi,
otherwise download and run Setup.exe
 For Macintosh computers:
- Download Whisky, unzip it and copy Whysky to the Application folder.
- (Let me know if the Whisky link above becomes unavailable)
- Download TRAD.msi
- Double-click Whisky and follow the concise instructions to run the downloaded TRAD.msi file.
- Whysky includes a "winetricks" button. Click it and click "Dlls" tab. Select "dotnet48" (which means .NET Framework 4.8) and click "Run". It could take 10 minutes to finish installation. A Terminal window will display the program. Wait until the Terminal window returns to the Linux command prompt.
- You can now double-click "TRAD" (which has a green arrow above) to run TRAD. You may need to wait for 10 seconds the first time you do it. During this ~10 seconds, there seems no response, but TRAD will eventually start.
- Once TRAD starts, click "Phylogenetics | TRAD", input a tree, e.g., ncov-2019.ml.tree, and click "OK".
Here are some screenshots of running TRAD on an M2 MAC (M1, M2, M3 and M4 MACs work the same way).
The first dialog for inputing a tree for TRAD:
The observed and fitted relationship between D (root-to-tip distance) and T (Collection time)
The predicted r (evolutionary rate) and T (Collection time):
The rooted and dated tree:
 For 64-bit Linux computers:
- Click the App Store or Package Manager, and choose wine to install.
- (alternatively, issue the command sudo apt install --install-recommends winehq-stable)
- At the end of wine installation, you may be prompted to instlal Mono. Acept to install
- Download TRAD.msi
- wine msiexec /i TRADSetup.msi
- TRAD is now ready to run.
- Here are more information on msiexec
Usage after installation:
- Click 'Phylogenetics | TRAD
- Input: a phylogenetic tree in Newick format, with collection time at the end of the sequence name. A test file Test_Fig1.dnd is provided.
- Output: evolutionary rate, the time of origin of the most recent common ancestor, the most likely rooting point
Warning:
- GenBank contains fake SARS-CoV-2 genomes. See my paper for details. You should not include such genomes in your analysis.
- You should include only viral sequences isolated from natural hosts, not from specially treated experimental animals.
- Do not include genomes from viruses that have been preserved for a long time (e.g., by deep-freezing) and then thawed and used in experiments. Such viruses have been frozen in evolution. Their genomes will mislead you to a very slow evolutionary rate and erroneous dating of the common ancestor.
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