The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

Protein sequence alignment is the task of identifying evolutionarily or structurally related
positions in a collection of amino acid sequences. Although the protein alignment problem …

We describe a new program for the alignment of multiple biological sequences that is both
statistically motivated and fast enough for problem sizes that arise in practice. Our F ast S …

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

We describe a novel model and algorithm for simultaneously estimating multiple molecular
sequence alignments and the phylogenetic trees that relate the sequences. Unlike current …

One of the oldest problems in linguistics is reconstructing the words that appeared in the
protolanguages from which modern languages evolved. Identifying the forms of these …

Insertions and deletions constitute the second most important source of natural genomic
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …

Background Two central problems in computational biology are the determination of the
alignment and phylogeny of a set of biological sequences. The traditional approach to this …

It is believed that most modern mammalian lineages arose from a series of rapid speciation
events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the …

We present a new probabilistic model of sequence evolution, allowing indels of arbitrary
length, and give sequence alignment algorithms for our model. Previously implemented …