Mathematical Hierarchies and Biology

Ancestor-descendant relations and incompatible data: Motivation for research in discrete mathematics by G. F. Estabrook Krohn-Rhodes theory, hierarchies & evolution by C. L. Nehaniv and J. L. Rhodes Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages by M. Bonet, C. Phillips, T. Warnow, and S. Yooseph Reconciled trees and incongruent gene and species trees by R. D. M. Page and M. A. Charleston Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees by O. Eulenstein, B. Mirkin, and M. Vingron Fitting models of intron evolution to aldehyde dehydrogenase data by A. Rzhetsky, F. J. Ayala, L. C. Hsu, C. Chang, and A. Yoshida Dissimilarity maps and substitution models: Some new results by V. Moulton, M. Steel, and C. Tuffley The performance of the neighbor-joining method of phylogeny reconstruction by K. Atteson Concerning the NJ algorithm and its unweighted version, UNJ by O. Gascuel Order distances in tree reconstruction by A. Guenoche Circular orders of tree metrics, and their uses for the reconstruction and fitting of phylogenetic trees by V. Makarenkov and B. Leclerc Estimation of missing distances in path-length matrices: Problems and solutions by P.-A. Landry and F.-J. Lapointe Complexity issues in hierarchical optimization by P. M. Pardalos and X. Deng Nesticity by P. Hansen and D. de Werra Phylogeny graphs of arbitrary digraphs by F. S. Roberts and L. Sheng Agreement metrics for trees revisited by E. Kubicka, G. Kubicki, and F. R. McMorris Sparse dynamic programming for maximum agreement subtree problem by T. M. Przytycka The median function on weak hierarchies by F. R. McMorris and R. C. Powers Towards a theory of holistic clustering by A. W. M. Dress On hierarchies and hierarchical classes models by I. van Mechelen, S. Rosenberg, and P. De Boeck The construction of globally optimal ordered partitions by L. Hubert, P. Arabie, and J. Meulman Multiple trees: Fitting two or more tree structures to proximity data by J. D. Carroll and G. De Soete Linear embedding of binary hierarchies and its applications by B. Mirkin Learning algorithms generating multigranular hierarchies by A. Meystel Index.