Simple fast algorithms for the editing distance between trees and related problems
SIAM Journal on Computing
Alignment of trees: an alternative to tree edit
Theoretical Computer Science
The Tree-to-Tree Correction Problem
Journal of the ACM (JACM)
Information Processing Letters
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
An algebraic view of the relation between largest common subtrees and smallest common supertrees
Theoretical Computer Science
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast RNA Structure Alignment for Crossing Input Structures
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Semantics and Ambiguity of Stochastic RNA Family Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
How to compare arc-annotated sequences: the alignment hierarchy
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
A linear tree edit distance algorithm for similar ordered trees
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Local exact pattern matching for non-fixed RNA structures
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
RNA tree comparisons via unrooted unordered alignments
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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We present two enhancements to Jiang's tree alignment algorithm, motivated by experience with its use for RNA structure alignment. One enhancement is the introduction of an affine gap model, which can be accommodated with a runtime increase by a constant factor. The second enhancement is a speed-up of the alignment algorithm when certain nodes in the trees are pre-aligned by a so-called anchoring. Both enhancements are included in a new implementation of the tool RNAforester. We also argue that tree alignment should be parameterized by a user-described set of edit operations, generalizing over the traditional, atomic edit operations.