Efficient generation of uniform samples from phylogenetic trees

Abstract

In this paper, we introduce new algorithms for selecting taxon (leaf) samples from large phylogenetic trees, uniformly at random, under certain biologically relevant constraints on the taxa. All the algorithms run in polynomial time and have been implemented. The algorithms have direct applications to the evaluation of phylogenetic tree and supertree construction methods using biologically curated data. We also relate one of the sampling problems to the well-known clique problem on undirected graphs. From this, we obtain an interesting new class of graphs for which many open problems exist. © Springer-Verlag Berlin Heidelberg 2003.