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 …

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

A phylogenetic alignment differs from other forms of multiple sequence alignment because it
must align homologous features. Therefore, the goal of the alignment procedure should be …

I have addressed the biological rather than bioinformatics aspects of molecular sequence
alignment by covering a series of topics that have been under-valued, particularly within the …

Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence
alignment used by modern sequence aligners. Although effective in practice for both runtime …

Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with
the assumption being that as alignments improve, so will phylogenetic reconstructions. Over …

Minelli, A. 2000. The ranks and the names of species and higher taxa, or a dangerous inertia
of the language of natural history. Pages 339-351 in Cultures and institutions of natural …

We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test
phylogenetic relationships in the South American “lava lizards”(genus Microlophus) and …

The classic methodology of inferring a phylogenetic tree from sequence data is composed of
two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is …

For sequences that are highly divergent, there is often insufficient information to infer
accurate alignments, and phylogenetic uncertainty may be high. One way to address this …