Figure 1
From: Grammar-based distance in progressive multiple sequence alignment
Algorithm overview. The algorithm operates on a set of sequences S originally read in FASTA format. After a grammar-based distance matrix D is estimated, a minimal spanning tree T is constructed. The tree is used as a map for determining the order in which the sequence set is progressively aligned in A. Gaps in the alignment are grouped together using a sliding window resulting in A Adj . Several outputs are available, including the distance matrix and various sequence alignment formats.