Sentence examples for alignments programs from inspiring English sources

In theory, sequence alignment cannot be considered separately from phylogenetic inference (e.g. many alignments programs use a guide tree), but both problems are NP-hard 26, 27 and in practice most researchers have regarded tree building as a distinct step (but see 28– 30).

The alignments were performed using the CLUSTALW (1.81) Multiple Sequence Alignments program using default options unless stated otherwise.

For both simulated data sets, we align these reads using the four selected alignment programs.

On bacterial genomes however, these aligners might be slower than hash table based alignment programs.

Thus, alignment programs can be evaluated by their ability to correctly align these core blocks.

CLUSTALW multiple alignment programs (http://www.ddbj.nig.ac.jp and http://mobyle.pasteur.fr) were used to align the amino acid sequences.

For both alignment programs, gap opening and extension parameters were set to their defaults.

The optimization method is also used to compare distinct sequence alignment programs and distance functions.

Different alignment programs handle the issue of reporting unique hits or multiple hits differently.

Thus, a total of eight different versions of the alignment programs were tested (Table 1).

'SSAHA'GMAPMand, and 'Mosaik' are all-purpose sequence alignment programs, not necessarily optimized for SNP discovery.