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

Abstract The interface of protein structural biology, protein biophysics, molecular evolution,
and molecular population genetics forms the foundations for a mechanistic understanding of …

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 …

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species
distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the …

Amphibians are one of the most threatened vertebrate classes, yet at the same time new
species are being described every year, demonstrating that the number of existing species …

We infer phylogenetic relationships within Teioidea, a superfamily of Nearctic and
Neotropical lizards, using nucleotide sequences. Phylogenetic analyses relied on …

Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying
ancient proteins and comparing biochemical properties between parental or extinct species …

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies)
comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore …

Ecologists increasingly wish to use phylogenies, but are hampered by the technical
challenge of phylogeny estimation. 2. We present phyloGenerator, an open-source, stand …