Over the last 10 or more years, there has been a tremendous increase in the use of
computational techniques (many of which come directly from biology) for estimating …

Phylogenetic inference and evaluating support for inferred relationships is at the core of
many studies testing evolutionary hypotheses. Despite the popularity of nonparametric …

The amount of sequence data available to reconstruct the evolutionary history of genes and
species has increased 20-fold in the past decade. Consequently the size of phylogenetic …

The relative contribution of taxon number and gene number to accuracy in phylogenetic
inference is a major issue in phylogenetics and of central importance to the choice of …

We study the problem of learning a latent tree graphical model where samples are available
only from a subset of variables. We propose two consistent and computationally efficient …

Methods such as maximum parsimony (MP) are frequently criticized as being statistically
unsound and not being based on any “model.” On the other hand, advocates of MP claim …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

In this paper, we study the problem of learning phylogenies and hidden Markov models. We
call a Markov model nonsingular if all transition matrices have determinants bounded away …

We assess the phylogenetic potential of∼ 300,000 protein sequences sampled from Swiss-
Prot and GenBank. Although only a small subset of these data was potentially …

The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …