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. 2012 May 30;13:117. doi: 10.1186/1471-2105-13-117

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Copyright ©2012 Collingridge and Kelly; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Effect of generating MergeAlign consensus MSAs with increasing numbers of constituent alignments. Individual MSAs were generated for a set of 1000 randomly selected benchmark MSAs using either MAFFT FFT-NS-2 (grey lines) or MAFFT L-INS-i (black lines). MSAs were added to the consensus MSA in the order in which the matrices that generated them are ranked ( Additional file 2). As a result, the mean F-score of constituent MSAs (marked with triangles) drops as more alignments are included. However, the mean F-score of MSAs generated by MergeAlign (marked with circles) is relatively stable. Furthermore, MergeAlign outperforms M-Coffee (dashed line) on the same set of benchmark MSAs.