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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 …

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 …