Sentence examples for each group were aligned from inspiring English sources

Structures in each group were aligned by the multiple structure alignment function of RSmatch with default scoring matrices.

The proteins in each group were aligned using the Darwin multiple sequence alignment package (Gonnet, Hallett, et al. 2000; Gonnet, Korostensky, and Benner 2000).

The AUG 3' flanking sequences in each group were aligned and analyzed by the Weblogo program.

Sequences in each group were aligned (using ClustalW [30] and Dialign [31]) for careful inspection of their features.

The sequences of each group were aligned to obtain sequence logo of the translation initiation site using WebLogo 3, version 2.8.2 (http://weblogo.berkeley.edu/).edu/

Following the clustering, sequences within each group were aligned using MUSCLE.

Each group was aligned using ProMals (Pei and Grishin, 2007 ).

We assume that each group being aligned is monophyletic, which is potentially a problem once saturation is detected and less inclusive multiple sequence alignments are employed.

Then, each group was aligned separately using Muscle version 3.8.31 (Edgar 2004), and the aligned sequences of all the groups were concatenated and conserved blocks were obtained for phylogenetic analysis using Gblocks version 0.91 b (Castresana 2000) with default parameters.

The proteins in each orthologous group were aligned using MUSCLE with default parameters [ 51], and the alignments were then trimmed using trimAL [ 52] to remove poorly aligned regions, using the parameter "-automated1".

The nematode specific sequence profiles from each orthologous group were aligned to the corresponding reference sequence profiles using CLUSTALW[42].