Probabilistic Distances Between Trees

Probabilistic Distances Between Trees

Most existing measures of distance between phylogenetic trees are based on the geometry or topology of the trees. Instead, we consider distance measures which are based on the underlying probability distributions on genetic sequence data induced by trees. Monte Carlo schemes are necessary to calculate these distances approximately, and we describe efficient sampling procedures. Key features of ...

Corrigendum to: “Probabilistic Distances Between Trees”

Computing Distances between Probabilistic Automata

We present relaxed notions of simulation and bisimulation on Probabilistic Automata (PA), that allow some error ε . When ε = 0 we retrieve the usual notions of bisimulation and simulation on PAs. We give logical characterisations of these notions by choosing suitable logics which differ from the elementary ones, L and L ¬, by the modal operator. Using flow networks, we show how to compute the r...

Computing Distances between Evolutionary Trees

Supported in part by a CGAT (Canadian Genome Analysis and Technology) grant. Work done while the author was at McMaster University and University of Waterloo. Supported in part by NSF grant 9205982 and CGAT. Supported in part by NSERC Operating Grant OGP0046613 and CGAT. Supported in part by the NSERC Operating Grant OGP0046506 and CGAT. Supported in part by CGAT and NSERC Internation Fellowshi...

Distances Between Phylogenetic Trees: A Survey

Phylogenetic trees have been widely used in the study of evolutionary biology for representing the tree-like evolution of a collection of species. However, different data sets and different methods often lead to the construction of different phylogenetic trees for the same set of species. Therefore, comparing these trees to determine similarities or, equivalently, dissimilarities, becomes the f...