High-level description of our algorithm to calculate a multiple alignment of a set of input sequences

. ., . The algorithm calculates a first alignment using our novel approach and a second alignment with the greedy method previously used in DIALIGN. Finally, the alignment with the higher numerical score is returned. For the progressive method, , i.e. local gap-free pairwise alignments from the respective optimal pairwise alignments are considered. Fragments with a weight score above the average fragment score are processed first following a as described in the main text. Lower-scoring fragments are added later, provided they are consistent with the previously included high-scoring fragments. Note that the output of the sub-routine is a chain of fragments. This is equivalent to a pairwise alignment in the sense of DIALIGN.Copyright information:Taken from "DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment"http://www.almob.org/content/3/1/6Algorithms for Molecular Biology : AMB 2008;3():6-6.Published online 27 May 2008PMCID:PMC2430965.