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 …

Infections are one of the major selective pressures acting on humans, and host-pathogen
interactions contribute to shaping the genetic diversity of both organisms. Evolutionary …

Motivation: We present a new feature of the MAFFT multiple alignment program for
suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly …

We report a major update of the MAFFT multiple sequence alignment program. This version
has several new features, including options for adding unaligned sequences into an existing …

Multiple sequence alignment (MSA) is ubiquitous in evolution and bioinformatics. MSAs are
usually taken to be a known and fixed quantity on which to perform downstream analysis …

In early January 2020, the novel coronavirus (SARS-CoV-2) responsible for a pneumonia
outbreak in Wuhan, China, was identified using next-generation sequencing (NGS) and …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

Multiple sequence alignment (MSA) is a key modeling procedure when analyzing biological
sequences. Homology and evolutionary modeling are the most common applications of …

Confidence in molecular dating analyses has grown with the increasing sophistication of the
methods. Some problematic cases where molecular dates disagreed with paleontological …

Molecular phylogenetic inference is inherently dependent on choices in both methodology
and data. Many insightful studies have shown how choices in methodology, such as the …