ArrayPhyloViz

Phylogenetic tree

ⓘ Supports phylogenetic trees in Newick format, including those generated by CRISPRPhylo and other phylogenetic analysis tools. Unique leaf names serve as stable IDs for matching spacer arrays. Branch lengths and internal node support labels are preserved.

CRISPR arrays

ⓘ SpacerMap SVG exports from this version retain IDs, colors and positions. For older images, use the numbered array data.

Match leaf names

Load your tree and arrays to see matched, missing, and unassigned records.

Review and edit mapping

Several arrays may map to one leaf. Unassigned arrays remain in the project but are excluded from the figure. Leaves without arrays stay visible.

Array	Spacers	Tree leaf	Status

Edit and export

Your integrated figure starts here

Drag empty space to pan · Ctrl / ⌘ + wheel to zoom

Filename name

Tree layoutArray alignment

Tree width Label space Array width Row spacing

Label sizeBranch weight

Default branch color

Use branch lengths Internal node labels / support Preserve SpacerMap style Spacer IDs Row guides Export spacer legend Shared-spacer links

Shared-spacer link width

Merge arrays by leaf

Leaf

Map two or more arrays to the same leaf to merge or reorder them.

Branch lengths are used only when every edge has a nonnegative length and at least one is positive. Spacer widths show order, not genomic distance.

SVG includes editable project data. Save JSON to reopen your exact view.

A QUICK GUIDE

How are tree leaves and arrays aligned?

Matching uses original Newick leaf names, not file order or display aliases. Exact matching is the default. Optional suffix matching strips _CRISPR1 or _array2; case-insensitive matching refuses ambiguous names. Under Review and edit mapping, Assign by leaf matches the part before the first underscore to an exact original tree leaf name: 702_NZ_JOLF01000035_1 maps to 702. Arrays without a matching leaf become Unassigned and are excluded from the figure. Multiple arrays form a group centered on their tree leaf. Merge all by leaf combines each leaf's arrays into one row, retaining their current display order and every spacer copy. Individual merge and ordering controls remain available; mapping and merging can be undone.

Can I reuse a SpacerMap visualization?

Download an SVG from SpacerMap and import it under CRISPR arrays. Its embedded metadata retains spacer IDs, colors and alignment positions. Older SVGs and PNG/JPEG screenshots do not contain enough reliable data for editing. For plain text input, supply one array per line as array_name spacer1,spacer2,.... SpacerMap's Download numbered file contains only a Spacer_ID / Spacer_Sequence mapping, not array membership, and cannot reconstruct the arrays. To use a CRISPRPhylo tree, download its Newick (.nwk) file and import it under Phylogenetic tree.

How do alignment and shared-spacer links work?

Left and Right align rows to the corresponding edge. Justify uses the same repeated-spacer column assignment as SpacerMap and preserves spacer order; it falls back to right alignment when no spacer ID is repeated. Spacer sizes stay consistent across Left, Right and Justify. Justify expands the horizontal canvas when needed to prevent overlap. Source positions uses imported position data when available. Shared-spacer links are enabled for new projects; saved projects retain their chosen setting.

What edits are retained in exports?

SVG and project JSON retain tree structure, original IDs, mapping, colors, positions, display labels, reversals and folded clades. PNG and PDF export the complete figure, independent of screen zoom. Newick exports the full tree in its edited child order, preserving branch lengths and original names; display annotations live in the project.

What are the scope and limits?

Supports rectangular or slanted trees with up to 1,000 leaves, 1,500 arrays and 20,000 spacer instances. It does not infer a new tree, reroot, or change branch lengths. Newick bracket comments are ignored; plain internal support labels are retained. PNG exports are limited to 32 million pixels and 16,000 pixels per side after applying the export scale; use SVG for large figures. Commit creates the figure and saves a project snapshot to the server. Download a project JSON, or use Save changes to save a later snapshot and reopen it from My Jobs. Later edits require a new save; anyone with the private link can open the saved project.