This review provides an overview on the development of Multiple sequence alignment
(MSA) methods and their main applications. It is focused on progress made over the past …

Aims The most common metric of arbuscular mycorrhizal fungal (AMF) abundance is percent
root length colonized (PRLC) by mycorrhizal structures. Frequently, plants with greater …

The assignment of functions to uncharacterized proteins discovered in genome projects
requires easily accessible tools and computational resources for large-scale, user-friendly …

Although much work has linked the human microbiome to specific phenotypes and lifestyle
variables, data from different projects have been challenging to integrate and the extent of …

To better determine the history of modern birds, we performed a genome-scale phylogenetic
analysis of 48 species representing all orders of Neoaves using phylogenomic methods …

Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and
comparative genomics studies. However, from the same set of sequences different MSAs …

The early evolutionary history of the chloroplast lineage remains an open question. It is
widely accepted that the endosymbiosis that established the chloroplast lineage in …

Evolutionary analyses require sequence alignments that correctly represent evolutionary
homology. Evolutionary and structural homology are not the same and sequence alignments …

New microbial genomes are constantly being sequenced, and it is crucial to accurately
determine their taxonomic identities and evolutionary relationships. Here we report …

In this paper, we introduce a new and highly scalable algorithm, PASTA, for large-scale
multiple sequence alignment estimation. PASTA uses a new technique to produce an …