With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the
computational challenge of efficiently and accurately constructing multiple genome …

Multiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple
Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that …

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 …

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

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at
varying evolutionary distances, as demonstrated by applications to multiple genomes. Two …

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

In this paper we present several web-based tools to identify conserved patterns in
sequences. In particular we present details on the functionality of PROMO version 2.0, a …

To compare entire genomes from different species, biologists increasingly need alignment
methods that are efficient enough to handle long sequences, and accurate enough to …

The suffix tree is one of the most important data structures in string processing and
comparative genomics. However, the space consumption of the suffix tree is a bottleneck in …