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
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
Computing Similarity between RNA Structures
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
A fast algorithmic technique for comparing large phylogenetic trees
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Drawing (Complete) Binary Tanglegrams
Graph Drawing
Generalized Binary Tanglegrams: Algorithms and Applications
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Untangling Tanglegrams: Comparing Trees by Their Drawings
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Untangling Tanglegrams: Comparing Trees by Their Drawings
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Have your spaghetti and eat it too: evolutionary algorithmics and post-evolutionary analysis
Genetic Programming and Evolvable Machines
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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. We introduce a constrained form of this problem in which a partial mapping of a set of nodes 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 we give a polynomial-time algorithm.