A QUICK GUIDE
Which input should I use?
Paste or upload the processed spacer CSV exported by CRISPRPrep. Keep the original column headers, including strain, array, orientation, spacer and repeat information. Use Load example to try a prepared dataset, then click Commit.
How do I choose the analysis settings?
Select GraphMSA or CRISPRFormer. For CRISPRFormer, choose the model profile that matches your data. Repeat grouping distance sets the maximum repeat edit distance; 0 groups identical repeats only. Enable Also build array trees if you also want a ZIP of individual array trees.
How do I inspect and download the tree?
Drag the tree to pan and use Ctrl / ⌘ + scroll to zoom. Use Midpoint root, Root on branch or Restore original root to adjust the displayed rooting. Midpoint root requires known, nonnegative branch lengths and a positive tree diameter. Root changes apply to the current preview and downloads; reopening the saved job restores its original tree. Download the strain tree as SVG, PNG or Newick (.nwk). Optional array trees are provided as a ZIP download.
How can I return to my results?
Keep the private results link shown after Commit, or retrieve the job from My Jobs. The link restores the saved tree and available downloads. The original input and the full set of form settings are not restored. For detailed instructions, read the CRISPRPhylo documentation.