Note that a recent study suggested that it is beneficial to include both orthologs and paralogs in the multiple sequence alignment used as input for correlated mutation analysis [ 78].
Data for >3 clones sequenced in both directions were compared by using the multiple sequence alignment function in Lasergene version 7.2 software (DNASTAR, Madison, WI, USA) (31, 32 ).
The multiple sequence alignments improve the average prediction to 71.9%.
The multiple sequence alignments were manually edited.
The multiple sequence alignment is available as supplementary dataset S1.
Based on the multiple sequence alignment techniques, we observed similarities in the sequences.
Besides alignment quality the sequence composition of the multiple sequence alignment could potentially affect results.
The multiple sequence alignment tool Clustal X2.0 was used for multiple protein sequence alignment [ 27].
The multiple sequence alignment of the soybean expansins.
MXRG prepared all the multiple sequence alignments for this study.
