MaxAlign - 1.1

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.


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