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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
 

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:
  1. Download and unzip TRAD.zip to a directory, say ~/TRAD.
  2. 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 *
  3. 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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