Gene duplication is postulated to have played a major role in the evolution of biological
novelty. Here, gene duplication is examined across levels of biological organization in an …

Conifers have dominated forests for more than 200 million years and are of huge ecological
and economic importance. Here we present the draft assembly of the 20-gigabase genome …

Comparative genomics in general and orthology analysis in particular are becoming increasingly
important parts of gene function prediction. Although not yet being in its final form, our …

We present GSR, a probabilistic model integrating gene duplication, sequence evolution,
and a relaxed molecular clock for substitution rates, that enables genomewide analysis of …

Background The use of short reads from High Throughput Sequencing (HTS) techniques is
now commonplace in de novo assembly. Yet, obtaining contiguous assemblies from short …

The genome sequence of Populus trichocarpa was screened for genes encoding cellulose
synthases by using full-length cDNA sequences and ESTs previously identified in the tissue …

Gene tree and species tree reconstruction, orthology analysis and reconciliation, are problems
important in multigenome-based comparative genomics and biology in general. In the …

Phylogeny is both a fundamental tool in biology and a rich source of fascinating modeling
and algorithmic problems. Today's wealth of sequenced genomes makes it increasingly …

Lateral gene transfer (LGT)—which transfers DNA between two non-vertically related
individuals belonging to the same or different species—is recognized as a major force in …

Motivation: New generation sequencing technologies producing increasingly complex datasets
demand new efficient and specialized sequence analysis algorithms. Often, it is only the ‘…