Sentence examples for alignment the maximum from inspiring English sources
For each block in the reference alignment, the maximum score obtained by any of the programs was selected and these maximal block scores were then averaged over the whole alignment.
Due to the short length of the alignment, the maximum likelihood phylogenetic analysis of this protein was inconclusive.
For these analyses, we extensively relied on the egglib package [ 75] to implement the following pipeline: First, for every alignment the maximum likelihood phylogeny was inferred at the nucleotide level using PhyML 3.0 [ 76] under the GTR-Γ substitution model.
Rather than sum over many multiple alignments, for each gene segment I use the alignment with the maximum score as detailed below.
To analyze a given alignment A of extant sequences, we first determine the probability of the alignment under the maximum likelihood estimate (MLE) of the parameters for the coding model, p C =maxθ C Pr(A|Coding,θ C ).
A local algorithm allows finding the optimal alignment of two fragments of the studied sequences, whereby the regions before and after the fragments forming the alignment with the maximum weight are not taken into account when the weight is calculated.
The read-mapping algorithm reports one or more alignments for each read within a scoring threshold, commonly expressed as the minimal acceptable significance of the alignment, or the maximum acceptable number of differences between the read and the reference genome.
Furthermore, we applied 3D alignment using the maximum common subgraph.
We thus inferred phylogenetic trees from the poa alignment under the maximum likelihood criterion with RAxML version 7.04 [54].
A neighbor-joining (nj) phylogenetic tree of PCSK9 from 14 primate species was reconstructed from the coding sequence alignment, and the maximum likelihood estimate of the tree topology was acquired using the 'hyphy' package [34].
For each instance, the alignment with the maximum EC in five runs was chosen as its final result.
