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.