Mathematical Hierarchies and Biology, Vol. 37 Book

	Foreword
	Preface
	Ancestor-Descendant Relations and Incompatible Data: Motivation for Research in Discrete Mathematics	1
	Krohn-Rhodes Theory, Hierarchies & Evolution	29
	Inferring Evolutionary Trees from Polymorphic Characters, and an Analysis of the Indo-European Family of Languages	43
	Reconciled Trees and Incongruent Gene and Species Trees	57
	Comparison of Annotating Duplication, Tree Mapping, and Copying as Methods to Compare Gene Trees with Species Trees	71
	Fitting Models of Intron Evolution to Aldehyde Dehydrogenase Data	95
	Dissimilarity Maps and Substitution Models: Some New Results	111
	The Performance of the NJ Method of Phylogeny Reconstruction	133
	Concerning the NJ Algorithm and Its Unweighted Version, UNJ	149
	Order Distances in Tree Reconstruction	171
	Circular Orders of Tree Metrics, and Their Uses for the Reconstruction and Fitting of Phylogenetic Trees	183
	Estimation of Missing Distances in Path-Length Matrices: Problems and Solutions	209
	Complexity Issues in Hierarchical Optimization	219
	Nesticity	225
	Phylogeny Graphs of Arbitrary Digraphs	233
	Agreement Metrics for Trees Revisited	239
	Sparse Dynamic Programming for Maximum Agreement Subtree Problem	249
	The Median Function on Weak Hierarchies	265
	Towards a Theory of Holistic Clustering	271
	On Hierarchies and Hierarchical Classes Models	291
	The Construction of Globally Optimal Ordered Partitions	299
	Multiple Trees: Fitting Two or More Tree Structures to Proximity Data	313
	Linear Embedding of Binary Hierarchies and Its Applications	331
	Learning Algorithms Generating Multigranular Hierarchies	357
	Index	385