An multiple alignment tool based on the alignment of sequence triplets
Overviewaln3nn 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.
The aln3nn software tool is designated to align both nucleic acid and amino acid sequences. If RNA sequences are aligned the tool provides a special feature that is to use additional structural information. This makes sense because many ncRNA evolve very quickly which means that sequence information is not always reliable. Structure in contrast evolves slowly and is therefore more stable.
PublicationKruspe, M., Stadler, P.F. (2006) Progressive sequence alignments from Triplets, submitted