Within the next decade, the genomes of 1.8 million eukaryotic species will be sequenced.
Identifying genes in these sequences is essential to understand the biology of the species …

Most sequencing data analyses start by aligning sequencing reads to a linear reference
genome, but failure to account for genetic variation leads to reference bias and confounding …

Large-scale genomics requires highly scalable and accurate multiple sequence alignment
methods. Results collected over this last decade suggest accuracy loss when scaling up …

Motivation The estimation of large multiple sequence alignments (MSAs) is a basic
bioinformatics challenge. Divide-and-conquer is a useful approach that has been shown to …

Multiple sequence alignment (MSA) is a critical step in the study of protein sequence and
function. Typically, MSA algorithms progressively align pairs of sequences and combine …

Phylogeny estimation is a major step in many biological studies, and has many well known
challenges. With the dropping cost of sequencing technologies, biologists now have …

Motivation Multiple sequence alignment (MSA) is a basic step in many bioinformatics
pipelines. However, achieving highly accurate alignments on large datasets, especially …

Background The alignment of large numbers of protein sequences is a challenging task and
its importance grows rapidly along with the size of biological datasets. State-of-the-art …

Multiple sequence alignment tools struggle to keep pace with rapidly growing sequence
data, as few methods can handle large datasets while maintaining alignment accuracy. We …

Motivation For the alignment of large numbers of protein sequences, tools are predominant
that decide to align two residues using only simple prior knowledge, eg amino acid …