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EBI T-Coffee

T-Coffee (tree-based consistency target function for alignment assessment) is a program that performs multiple sequence alignments on DNA, RNA and protein sequences. The most unique feature of the program is that it allows users to combine the results with the results of different alignment programs. You can then provide a printout based on the similarities between these results. The T-Coffee API of the European Bioinformatics Institute makes these functions available through SOAP and REST protocols.
EBI T-Coffee Screenshot

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