Sentence examples for for the whole alignment from inspiring English sources
Mitochondrial branch lengths were estimated for the whole alignment (all substitutions), as well as nonsynonymous (dN) and synonymous substitutions (dS): see methods for details.
This algorithm was input a matrix containing the site log-likelihoods for all 181 topologies tested (obtained by placing the Aquificales in all possible positions in the backbone bacterial phylogeny) and for the whole alignment.
We then compared the log-likelihood value of a model (Goldman and Yang model, hereon called G&Y) [ 45] that assumes one ω for the whole alignment and phylogenetic tree to a model that estimates an ω value for each branch of the phylogenetic tree (hereon called the free-ratio model FRM).
If the related to these locations are augmented in a single string, the Primary Pole Score for that particulate PP is defined as the alignment score of that augmented string (with respect to the scoring matrix used for the whole alignment).
Therefore, there are eight (λ, K) parameters that help to evaluate the alignments (four for the forward alignment sense and four for the reverse complementary alignment sense): (λ FW, K FW ) for the forward sense and (λ RC, K RC ) for the reverse complementary sense respectively, that are used for evaluating the score of the whole alignment.
This network reconstruction could be achieved by different means, either through the recoding of the PAMs features in a matrix of characters or by realizing a Splitstree analysis (for instance) of the whole alignments of Ty3/Gypsy and Retroviridae sequences.
If not noted otherwise, identities are reported for the whole alignments i based on truncated alignments Thirty-six (53.7 %) of the reconstructed genes are homologous to previously functionally characterized genes of WSSV (and other organisms in the case of IAP.
The testing showed that there is a little saturation in the whole alignment for each of four analysed nucleotide data sets.
While the Viterbi decoding assigns gain only if the whole alignment is correctly predicted, posterior decoding assigns gain +1 for each correctly identified alignment column.
For the whole database alignment maximum likelihood trees were calculated using the MPI version of raxmlHPC [24] on a Linux cluster of 32 PCs containing 32 AMD Opteron cpus.
