Phylogeny subsets

This tool provides a simple way to produce distributions of trees with subsets of taxa. If larger subsets are required you can download full trees.

The tool first trims to a subset, and then samples trees from a chosen pseudo-posterior distribution. Note that any further analyses should only be conducted with a large sample of trees.


  1. Select species from the list which follows the taxonomy. Then copy and paste or drag and drop them into the box to the right.
    • Alternatively, download the taxonomy file for your group and paste species names from the “Scientific” column.
    • Please note: If you have different names, you will have to resolve to the available list.
  2. Choose a tree distribution (see paper for details).
  3. Select the number of trees to download (defaults to minimum of 100)
  4. Click “Get Trees” to download a zipped set of randomly selected trees with metadata including accession numbers and citations to original
  5. Please wait a minute then check the job status using your email address and job ID. If the download is complete, then you can download the trees. If the trees are not ready, please wait another minute and check the status again.

Results taking longer than expected?
Traffic volume may result in longer processing times. If you don't recieve an email with the completed subset trees within 24 hours, please contact us.


Note: Once completed, a link to the generated phylogeny subsets will be emailed to the address provided.

Note: We need a minimum of 100 and a maximum 10,000


Check the status of your job request here

e.g. tree-pruner-ade65c04-65fc-4028-a2bb-8da4d560bb97