The phrase "alignment the program" is not correct in written English.
It seems to be a fragment and lacks proper grammatical structure.
Example: "We need to ensure the alignment of the program with our goals."
Alternatives: "align the program" or "program alignment."
For those transcripts without any alignment, the program runs an Open Reading Frame (ORF) prediction step.
Among the methods for global multiple alignment, the program MAFFT [ 21, 22] performed remarkably well, not only on globally, but also on locally related sequences.
From an RNA alignment, the program creates weight matrices corresponding to different parts of the molecule, as defined by users, and finds all sequences matching these matrices above a certain score threshold.
However, DIALIGN uses a greedy approach only for multiple alignment where an exact solution is not feasible, but for pairwise alignment, the program returns an optimal alignment with respect to the underlying objective function.
To rate the alignment programs or program options, we ranked these scores after averaging over all datasets.
The DNA alignments were then computed based on the protein alignments using the program PAL2NAL [ 54].
Visual inspection of the alignments using the program MEGA1.4 [ 63] helped in refinement of the final alignments.
For the generation of multiple sequence alignments (MSAs) the program M-Coffee [ 32] was used.
Bayesian phylogenetic analyses were performed on these grouped aa alignments using the program p4 [ 36].
Phylogenetic trees were constructed from the alignments using the program PAUP* [ 57] and these were displayed in TreeView [ 58].
The choice of the alignment program depends on the biological application and on the type of sequencing technology used to generate the data.
