The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins
have long been and are still important issues in bioinformatics. To rapidly construct a …

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 …

Whole-genome sequences are now available for many microbial species and clades,
however existing whole-genome alignment methods are limited in their ability to perform …

Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …

Edward Jenner and his contemporaries believed that his variolae vaccinae originated in
horses and molecular analyses show that modern vaccinia virus (VACV) strains share …

Background Recent methods have been developed to perform high-throughput sequencing
of DNA by Single Molecule Sequencing (SMS). While Next-Generation sequencing methods …

Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity,
adaptability and growth have made them a global renewable resource of fibre and energy …

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

Sex determination evolved to control the development of unisexual flowers. In agriculture, it
conditions how plants are cultivated and bred. We investigated how female flowers develop …

We describe MUSCLE, a new computer program for creating multiple alignments of protein
sequences. Elements of the algorithm include fast distance estimation using k mer counting …