Maximizing the size of gap-free columns by selecting an optimal subset of sequences in an alignment.
The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience
for bioinformatical studies. In phylogenetic analyses, for instance, gapped columns are often
discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment
prior to such analyses. Specifically, it maximizes the number of characters that are present in
gap-free columns - alignment area - by selecting an optimal subset of sequences. MaxAlign can be
used prior to any phylogenetic analysis as well as in other situations where this form of
alignment clean up is useful, such as the presence of badly aligned or truncated sequences.