O(n2.5) time algorithms for the subgraph homeomorphism problem on trees
Journal of Algorithms
Tree graphs of RNA secondary structures and their comparisons
Computers and Biomedical Research
On distances between phylogenetic trees
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Journal of Algorithms
Algorithmics and applications of tree and graph searching
Proceedings of the twenty-first ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems
Algorithms on Trees and Graphs
Algorithms on Trees and Graphs
A Structure-Based Search Engine for Phylogenetic Databases
SSDBM '02 Proceedings of the 14th International Conference on Scientific and Statistical Database Management
Nice Drawings for Planar Bipartite Graphs
CIAC '97 Proceedings of the Third Italian Conference on Algorithms and Complexity
Visualising phylogenetic trees
AUIC '06 Proceedings of the 7th Australasian User interface conference - Volume 50
A fast algorithmic technique for comparing large phylogenetic trees
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Seeded tree alignment and planar tanglegram layout
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Comparing trees via crossing minimization
Journal of Computer and System Sciences
Efficient chaining of seeds in ordered trees
IWOCA'10 Proceedings of the 21st international conference on Combinatorial algorithms
Forest alignment with affine gaps and anchors
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Efficient chaining of seeds in ordered trees
Journal of Discrete Algorithms
Hardness of approximation and integer programming frameworks for searching for caterpillar trees
CATS '11 Proceedings of the Seventeenth Computing: The Australasian Theory Symposium - Volume 119
Forest alignment with affine gaps and anchors, applied in RNA structure comparison
Theoretical Computer Science
Hardness of approximation and integer programming frameworks for searching for caterpillar trees
CATS 2011 Proceedings of the Seventeenth Computing on The Australasian Theory Symposium - Volume 119
Neighborhood-Preserving mapping between trees
WADS'13 Proceedings of the 13th international conference on Algorithms and Data Structures
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The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the "seeds") in one tree to a corresponding set of nodes in the other tree is given, and present efficient algorithms for both ordered and unordered trees. Whereas ordered tree matching based on seeded nodes has applications in pattern matching of RNA structures, unordered tree matching based on seeded nodes has applications in co-speciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.