High-throughput genomic sequencing is rapidly changing the field of phylogenetics by
decreasing the cost and increasing the quantity and rate of data collection by several orders …

K+ channel principal subunits are by far the largest and most diverse of the ion channels.
This diversity originates partly from the large number of genes coding for K+ channel …

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 …

In the analysis of sequence-based data matrices, the use of different methods of treating
gaps has been demonstrated to in? fluence the resulting phylogenetic hypothe? ses (eg …

Evaluating the accuracy of multiple sequence alignment (MSA) is critical for virtually every
comparative sequence analysis that uses an MSA as input. Here we present the GUIDANCE …

Advocates of conditional combination have argued that testing for incongruence between
data partitions is an important step in data exploration. Unless the partitions have had …

The ability to accurately predict gene function based on gene sequence is an important tool
in many areas of biological research. Such predictions have become particularly important …

Phylogenetic analysis of large datasets using complex nucleotide substitution models under
a maximum likelihood framework can be computationally infeasible, especially when …

The explosive growth of genomic data provides an opportunity to make increased use of
protein markers for phylogenetic inference. We have developed an automated pipeline for …