An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction

Phylogeny reconstruction on a genome scale remains computationally challenging even for closely related organisms. Here we propose an alignment-free pairwise distance measure, K_r, for genomes separated by less than approximately 0.5 mismatches/...

The role of phylogeny in guiding comparative studies is rapidly growing in the post genomic era. Most phylogeny reconstruction methods though, assume a single tree underlying a given alignment of sequences. However, when events such as recombination ...

Next generation sequencing (NGS) technologies have generated enormous amount of shotgun read data and assembly of the reads can be challenging, especially for organisms without template sequences. We study the power of genome comparison based on shotgun ...