WebPro-Coffee is a particular mode of T-Coffee designed to align specific functional DNA sequences, in particular regulatory regions. To run Pro-Coffee by default, just use command 1. In order to adjust the quality of the alignment, Pro-Coffee allows you to modify gap penalties (gap-opening and/or gap-extension) with specific flags (command 2). WebYou can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment ( M-Coffee ). T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information ( 3D-Coffee/Expresso ), profile ...
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