aln3nn is a progressive alignment tool that computes approximal exact solutions of the multiple alignment problem by the subsequent examination of sequence triplets. It is therefore predestinated to calculate more reliable alignments compared to the pairwise progressive sequence alignments approach. The alignment order is determined by means of a phylognetic network that is constructed using the NeighborNet package. To limit processor and memory usage we apply a standard divide-&-conquer approach.
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Kruspe, M., Stadler, P.F. (2006)
Progressive multiple sequence alignments from triplets
BMC Bioinformatics 2007, 8:254