Sentence examples for using the guide tree from inspiring English sources

In the second stage, the partial sequences were aligned to the full-length sequence profile using the guide tree generated during the first stage.

Build an alignment using the guide tree.

Using the guide tree obtained from *BEAST, we then performed the BPP analysis.

This compares the alignment generated using the guide tree, calculated using the embedded distances against the corresponding HOMSTRAD structural alignment.

Progressive alignment works by using the guide tree to align the next most closely related sequences to each other.

The alignment was refined using the guide tree illustrated in Figure 1 (an extended version of this tree is available online, as the Additional file 1).

For this we used the guide trees derived from (i) the full distance matrix, (ii) the SparseMap method and (iii) mBed.

The species tree, obtained from the Tree of Life website for the primates (tolweb.org/Primates/15963/1999.01.01), was used as the guide tree for the codeml program in the PAML package (version 4.5) (Yang 2007).

In order to determine relationships among tick serpins, a guide tree of 68 tick serpins sequences, 34 full-length serpins from this study, and 34 other tick serpins that were downloaded from GeneBank, and human α1-antitrypsin (out group, AAB59495) as an outlier were used to construct the guide tree using the neighbor joining method.

For each interval for which one unambiguous orthologous sequence could be identified in all four species, the sequences were multiply aligned using PRANK, estimating the guide tree directly from the data [ 92, 93].

This may be because the iterative tree-search used to define the guide tree produces a more accurate tree for these divergent sequences than the k-mer methods used by other MSAMs (supplementary fig. S3, Supplementary Material online), which in turn leads to groups of true and false pairwise homologies that nevertheless reflect the history of the sequences.