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TBRDist 2.0.0 (2026-03-23)

• Add RSPRDist() for rooted Subtree Prune-and-Regraft (rSPR) distances, wrapping the exact FPT algorithm (with cluster decomposition) of Whidden, Beiko & Zeh (2013). Supports exact distances, a linear-time 3-approximation, and maximum agreement forest output.
• Improve performance of USPRDist() by replacing string-based tree representation in the A* search with 256-bit integer tree numbers (Tromp encoding), giving O(1) equality and hash lookup.
• Add exact SPR distance lookup tables for trees with 4–9 leaves, eliminating A* search for small trees and subtrees encountered during reduction.
• Improve performance of USPRDist() A* search by replacing the multiset-based priority queue (pointer-chasing red-black tree) with a binary min-heap (priority_queue over a contiguous vector), giving better cache behaviour for queue operations.
• Reduce heap allocations in normalize_order() by replacing per-node map<int,unode*> with a 3-element inline array sort.
• Reduce heap allocations in TBR/replug branch-and-bound search by replacing list<unode*> neighbour storage with fixed-capacity inline arrays, replacing list/map book-keeping containers with vector/unordered_map, and allocating tree nodes from a block arena instead of individual new/delete.

TBRDist 1.0.3 (2025-11-28)

• Match updated CRAN policy.

TBRDist 1.0.2

• Import RdMacros package ‘Rdpack’.

TBRDist 1.0.1

• Address memory mismanagement in USPRDist().

TBRDist 1.0.0

• Initial implementation of distances on unrooted trees.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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