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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. 2021. TRAD: Tip-Rooting and Ancestor-Dating. http://dambe.bio.uottawa.ca/TRAD/TRAD.aspx
Xia, X. 2021. Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes. Viruses 13(9): 1790. |
Usage:
- Just a few clicks to install (see platform-specific installation below)
- Click 'Phylogenetics | TRAD
- Input: a phylogenetic tree in Newick format, with collection time at the end of the sequence name.
- Output: evolutionary rate, the time of origin of the most recent common ancestor, the most likely rooting point
 For Windows computers:
If your 64-bit Windows PC is new or updated, then you can launch TRAD now. Otherwise, install and run TRAD.
  For Macintosh and Linux computers with Mono installed:
- Download and unzip TRAD.zip to a directory, say ~/TRAD.
- Open a terminal windows and type the following commands:
sudo apt-get install mono-vbnc (Otherwise you may encounter an error unless you have issued the command before)
cd ~/TRAD
chmod 755 *
- Installation is now complete. For 64-bit MAC, type mono --arch=32 TRAD.exe (Tip from Dr. Rutger Vos) to run TRAD. For 32-bit Mac, just type mono TRAD.exe to run.
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