Consensus methods attempt to find the optimal multiple sequence alignment given multiple different alignments of the same set of sequences. There are two commonly used consensus methods, [http://www.tcoffee.org/Projects/mcoffee/ M-COFFEE] and [http://www.stevekellylab.com/software/mergealign MergeAlign].<ref name="mergealign">{{cite journal | doi = 10.1186/1471-2105-13-117 |vauthors=Collingridge PW, Kelly S | year = 2012 | title = MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments | journal = BMC Bioinformatics | volume = 13 | issue = 117 |pages=117 | pmid=22646090 | pmc=3413523 |doi-access=free }}</ref> M-COFFEE uses multiple sequence alignments generated by seven different methods to generate consensus alignments. MergeAlign is capable of generating consensus alignments from any number of input alignments generated using different models of sequence evolution or different methods of multiple sequence alignment. The default option for MergeAlign is to infer a consensus alignment using alignments generated using 91 different models of protein sequence evolution.
