Recent progress in genome-scale sequencing and comparative mapping raises new
challenges in studies of genome rearrangements. Although the pairwise genome …

The analysis of genome rearrangements provides a global view on the evolution of a set of
related species. We present a new algorithm called EMRAE (efficient method to recover …

Recently completed whole-genome sequencing projects marked the transition from gene-
based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an …

Multiple alignment of macromolecular sequences generalizes from N= 2 to N≥ 3 the
comparison of N sequences which have diverged through the local processes of insertion …

Although analysis of genome rearrangements was pioneered by Dobzhansky and
Sturtevant 65 years ago, we still know very little about the rearrangement events that …

Ancestral sequence reconstruction is a fundamental aspect of molecular evolution studies
and can trace small-scale sequence modifications through the evolution of genomes and …

Molecular evolution studies are usually based on the analysis of individual genes and thus
reflect only small-range variations in genomic sequences. A complementary approach is to …

We present a new pair-wise genome alignment method, based on a simple concept of
finding an optimal set of local alignments. It gains accuracy by not masking repeats, and by …

Background Identifying syntenic regions, ie, blocks of genes or other markers with
evolutionary conserved order, and quantifying evolutionary relatedness between genomes …

Motivation: The rapidly increasing set of sequenced genomes highlights the importance of
identifying the synteny blocks in multiple and/or highly duplicated genomes. Most synteny …