Sentence examples for by an alignment program from inspiring English sources
In practice, however, the true MSA is not available and an MSA has to be reconstructed from the sequence data by an alignment program.
Output of MSAs was then manually examined by visual inspection using an alignment program (MacVector, vers.11.1).11.1
Aligning step: The 1046 groups were aligned by Muscle, a multiple alignment program [ 23].
Second, the guide-tree reconstructed by the alignment program is generally a better estimator of the true topology than the tree reconstructed from gap patterns (Supplementary Fig. S6), indicating that the use of gap parsimony recovers less phylogenetic information than that already contained in the guide-tree.
Promoters of orthologous gene pairs were aligned by the local alignment program water from the EMBOSS package [ 33].
Prosup benchmark, prepared by Sippl's group, consists of 127 pairs of proteins with alignment by structural alignment program Prosup [38].
Act10 with one single residue exchange only (D2E) is more distant, which reflects the scores in the permutation matrix used by the alignment program.
First, the initial guide-tree produced by the alignment program is highly similar to the canonical tree (Supplementary Fig. S6), indicating that it carries a strong phylogenetic signal.
Furthermore, it is well established that the "optimal" MSA obtained by each alignment program reflects only one possible path out of many equally likely paths and many more suboptimal solutions (Landan and Graur 2007).
We presume that this is a consequence of the k-mer (k = 25) assembly process used by Trinity, perhaps creating isoform transcripts that are shorter than the long 454 reads from which they originally derive or possibly from read trimming by the alignment program.
