Crocodile

The genomes of three crocodilians provide insight into archosaur evolution

To provide context for the diversification of archosaurs—the group that includes crocodilians, dinosaurs, and birds—we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome …

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Alignathon: A competitive assessment of whole genome alignment methods

Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark datasets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem …

Coiled green tree snake

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, …

A cactus graph

Cactus Graphs for Genome Comparisons. Proceedings of RECOMB 2010

We introduce a data structure, analysis and visualization scheme called a cactus graph for comparing sets of related genomes Cactus graphs capture some of the advantages of de Bruijn and breakpoint graphs in one unified framework They naturally decompose the common substructures in a set …