Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …

The compilation of multiple metazoan genome sequences and the deluge of large-scale
expression data have combined to motivate the maturation of bioinformatics methods for the …

Divergence of gene function is a hallmark of evolution, but assessing functional divergence
over deep time is not trivial. The few alleles available for cross-species studies often fail to …

To connect human biology to fish biomedical models, we sequenced the genome of spotted
gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome …

Background Multiple genome alignment remains a challenging problem. Effects of
recombination including rearrangement, segmental duplication, gain, and loss can create a …

Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and
chimaeras, and the lack of established whole-genome sequences for the former has …

We present the first comprehensive analysis of a diploid human genome that combines
single-molecule sequencing with single-molecule genome maps. Our hybrid assembly …

As genomes evolve, they undergo large-scale evolutionary processes that present a
challenge to sequence comparison not posed by short sequences. Recombination causes …

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre
and fuel. We present an initial analysis of the∼ 730-megabase Sorghum bicolor (L.) …

Abstract Comparison of DNA sequences from different species is a fundamental method for
identifying functional elements in genomes. Here, we describe the VISTA family of tools …