This tool calculates multiple sequence alignment using MAFFT multiple sequence alignment tool.
MAFFT offers various multiple alignment strategies: the progressive ClusltaW like method, iterative refinement method with the WSP, and iterative refinment method using both the WSP and consistency scores. In general, there is a tradeoff between speed and accuracy. Faster methods are less accurate.In Chipster, MAFFT default selects the alignment method to be used based on the size of the sequence set to be aligned. Optionally, user can define a specific alignment strategy. Following strategies are available
In order to obtain more accurate alignments in difficult cases, three more complex alignment methods have been added toMAFFT. These methids use an objective function combining the WSP score (Gotoh) explained above and the COFFEE-like score (Notredame et al.), which evaluates the consistency between a multiple alignment and pairwise alignments (Katoh et al. 2005).
For pairwise alignment, three different types of algorithms are implemented, global alignment (Needleman-Wunsch), local alignment (Smith-Waterman) with affine gap costs (Gotoh) and local alignment with generalized affine gap costs (Altschul). The differences in the accuracy values among these methods are small. However, each of them has different characteristics, according to the algorithm in the pairwise alignment stage and thus the optimal method depends on the alignment case. The tree methods are:
More information can be found from the MAFFT home page. The input sequences must be in fasta format.
Output is a sequence file.