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Quickstart

This page is intentionally short. It points you to the minimal steps for common workflows.

I want to place sequences on a curated reference tree​

  1. Go to View reference trees in T-BAS.
  2. Choose the appropriate reference tree for your marker(s) and taxonomic scope.
  3. Upload your query sequences and metadata (when requested).
  4. Run phylogeny-based placement.
  5. Review placements in the interactive viewer and export results (MEP/PhyloXML, tables, sequences).
note

Some deployments may integrate placement workflows through DeCIFR portals and/or Galaxy.

I want to upload a custom tree​

  1. Prepare:
    • a tree file (e.g., Newick)
    • alignment(s) (single locus or multi-locus)
    • optional specimen/sequence metadata
  2. Use the Upload a custom tree entry point.
  3. Validate and submit.

I want to programmatically access results​

Use the DeCIFR REST Server and API: