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To study phylogenetic relationships of different OTUs, and the differences in the dominant species present in the different samples (i.e., groups), multiple sequences alignments were conducted using the MUSCLE software (Version 3.8.31) (Edgar 2004).
The aligner described in this study will enable scientists to rapidly generate robust multiple sequences alignments that are implicitly based upon the predicted secondary structure of the 16S rRNA molecule.
Multiple sequences alignments were done using ClustalW [ 26].
Multiple sequences alignments were built using Promals3D [ 72] and Muscle [ 73].
Multiple sequences alignments were obtained using T-COFFEE [ 67] or CLUSTAL_X [ 68].
The multiple sequences alignments were performed with MUSCLE software [ 73], implemented in MEGA5 (Molecular Evolutionary analysis) software [ 74].
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Multiple sequences alignment was done by ClustalW version 1.8.
Multiple Sequence Alignments.
The multiple sequence alignments improve the average prediction to 71.9%.
The multiple sequence alignments were manually edited.
Multiple sequence alignments were performed using ClustalW [46].
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