Sentence examples for contained in the alignment from inspiring English sources

The phylogenetic information contained in the alignment was visualised using likelihood mapping in TreePuzzle v4.0 ([ 37], ).

2) Mean of the energy z-scores of the individual sequences contained in the alignment (meanz ).

Computing SBMs based on D observed makes most use of the gap information contained in the alignment.

Hence we can interpret q as a reliability measure for the phylogenetic information contained in the alignment site (relative to C).

In the first step, T is restricted to the species contained in the alignment, and for each alignment column i, a relative substitution rate is estimated by numerically optimizing the likelihood of the tree:.

Here we use: 1) Average of the folding energies of the individual sequences contained in the alignment, computed by the minimum energy folding program RNAfold of the Vienna RNA Package, version 1.6 [ 14] (meanmfe ).

Any realistic reconstruction of phage evolutionary history needs to take into account HGT, and in this study, we use the information about gene content in phages with dsDNA genomes, in conjunction with phylogenetic signal contained in the alignments of phage-encoded proteins, to infer such a reticulated evolutionary history.

Thus, for a given alignment, the corresponding shortened alignment of length 10 is contained in the shortened alignment of length 25, which is contained in the shortened alignment of length 50, and so on.

Thirdly, although the short length of miRNAs also allows for the integration of gapped alignments in the SBM method, the method will only search for the gap patterns contained in the input alignment.

The genome-wide search was conducted with an E-value threshold of 1e-3 in all organisms contained in the RyhB alignment of the aforementioned dataset.

Of course, when we apply the Z-best strategy, we could miss a seed contained in the true alignment when a false match has a higher score.