SPR Analytics

The Moved Subtrees analytics window quantifies subtree-prune-and-regraft movement across neighboring input trees. Open it from Analysis -> Moved Subtrees.

An SPR move is one moved subtree that changes attachment between two neighboring trees. Rows report the moved subtree, source attachment, target attachment, and branch annotation values when available.

Tabs

Tab	Meaning	Main use
Overview	Summarizes unique moved subtrees, total SPR movement count, and active pair count.	Use this first to see how much movement the current tree sequence contains.
SPR Moves	Shows one row per SPR move between neighboring input trees.	Use this as the detailed event ledger for source/target placement context.
Recurrent Subtrees	Aggregates moved subtrees across all SPR moves and ranks them by repeat count.	Use this to identify taxa or clades that repeatedly move, then inspect their event rows in SPR Moves.

SPR Moves Table

The SPR Moves table reports one row per movement event:

Field type	Meaning
Moved subtree	Taxa or subtree that changes attachment.
Pivot edge	Edge around which the topology change is described.
Source attachment	Attachment context in the source tree before the move.
Target attachment	Attachment context in the target tree after the move.
Branch annotation values	Source-to-target values for the moved subtree and nearest parent branch, when available.
Movement steps	Local animation step range for the move.
Metrics	Path hops, path length, RF distance, and weighted RF distance when available.
MSA window range	Alignment-window context for MSA datasets.

Use this table to answer where a subtree moved from, where it moved to, and whether the source or target placement has supporting branch annotations. For example, if the trees carry bootstrap split-frequency labels or SH-aLRT branch-support values, the branch-value column shows the source-to-target values for the moved subtree and the nearest parent branch.

Branch Annotation Threshold

When branch support annotations are available, the analytics table can use a threshold to emphasize values above or below the selected branch annotation cutoff. Select the visible annotation in Style -> Geometry & Labels -> Branch Annotation.

The filters separate movement rows by whether the selected moved-subtree or parent-branch values are both above the threshold, mixed, both below the threshold, or missing. This helps distinguish movements involving stronger placement support from movements in weaker or unavailable support contexts.

Recurrent Subtrees

The Recurrent Subtrees table is a recurrence summary. It ranks moved subtrees by how often they participate in SPR moves. Columns include:

• SPR move count,
• tree-pair count,
• percentage of all SPR moves,
• total and average path hops,
• total and average path length.

Clicking a row marks that subtree in the tree view. A high recurrence count means that the same taxon or subtree participates in many SPR moves, but it is not a standalone detector. Interpret recurrent rows together with the detailed SPR Moves table, branch annotation values, and the animation.

This is especially useful for:

• rogue-taxon review,
• bootstrap replicate comparison,
• sliding-window recombination inspection,
• identifying repeated instability in a specific taxon group.

For rogue-taxon review, the recurrence table can show whether a candidate taxon or clade moves frequently, while the SPR Moves table shows whether those movements repeatedly switch between specific source and target attachment contexts and whether those placements are weakly or strongly supported.

CSV Exports

Export	Contents
Export SPR moves CSV	One row per SPR move.
Export recurrent subtrees CSV	One row per recurrent moved-subtree summary.

Exports are disabled when the current dataset does not contain rows for the selected analytics view.