The comparative method plays a central role in efforts to uncover the adaptive basis for
primate behaviors, morphological traits, and cognitive abilities. 1–4 The comparative method …

Cryptosporidium is one of the most common enteric protozoan parasites of vertebrates with
a wide host range that includes humans and domestic animals. It is a significant cause of …

Multiple sequence alignments are widely used to infer evolutionary relationships, enabling
inferences of structure, function, and phylogeny. Standard practice is to construct one …

Phylogenetic tree confidence is often estimated from a multiple sequence alignment (MSA)
using the Felsenstein bootstrap heuristic. However, this does not account for systematic …

Motivation: In the analysis of homologous sequences, computation of multiple sequence
alignments (MSAs) has become a bottleneck. This is especially troublesome for marker …

Phylogenetic relationships in Rosaceae have long been problematic because of frequent
hybridisation, apomixis and presumed rapid radiation, and their historical diversification has …

Background The quality of multiple sequence alignments plays an important role in the
accuracy of phylogenetic inference. It has been shown that removing ambiguously aligned …

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those
that are not very well conserved, requires the elimination of poorly aligned positions and …

Alignment quality may have as much impact on phylogenetic reconstruction as the
phylogenetic methods used. Not only the alignment algorithm, but also the method used to …

The evidentiary basis of the currently accepted classification of living amphibians is
discussed and shown not to warrant the degree of authority conferred on it by use and …