Sentence examples for each cluster were aligned from inspiring English sources

Protein sequences in each cluster were aligned with mafft_wrapper.py, each alignment was trimmed with pep_gblocks_wrapper.py, and all alignments were finally concatenated into a supermatrix.

The protein sequences of members in each cluster were aligned with ClustalW [ 43] and the alignments were used to generate neighbor-joining trees with the two-parameter substitution correction.

The 53 orthologs in each cluster were aligned using the MCoffee software [ 41] and the protein-alignments were back-translated to DNA-alignments using the TranslatorX software [ 42].

The complete mt genomes in each cluster were aligned with Mauve v.2.3.1 (Darling et al. 2010) using the full alignment option.

The nucleotide sequences for each cluster were aligned with PAL2NAL v.14 [ 155] to correspond to the trimmed amino acid alignment and ensure that the correct reading frame was maintained.

The amino acid sequences within each cluster were aligned using MUSCLE (version 3.8.31) [ 24].

Results: We present a novel algorithm that calculates clustered alignments; the method finds clusters of genes such that the genes within a cluster share a common alignment, but each cluster is aligned independently of the others.

The second is an algorithm which computes clustered alignments in which the genes within a cluster share a common alignment, but each cluster is aligned independently of the others.

Here, we present a novel approach that finds clusters of genes such that the genes within a cluster share a common alignment, but each cluster is aligned independently of the others.

Each cluster was aligned using the program ClustalW in European Bioinformatics Institute site.

Each cluster was aligned independently using a combination of CLUSTALX1.83 [ 14] and CLUSTALW1.81 [ 15] (see Additional file 2).