Sentence examples for input alignment from inspiring English sources

The input alignment contained 239 aligned amino acid positions from 768 sequences.

The technique of simulated annealing, by which an existing MSA produced by another method is refined by a series of rearrangements designed to find better regions of alignment space than the one the input alignment already occupies.

FINDMODEL [25] implemented the idea of MODELTEST for testing the best fit model for the input alignment of nucleotide sequences.

Aspergillus flavus was included when the alignments were constructed, but discarded for the RNAz searches because RNAz takes a maximum of six sequences in its input alignment.

For example, simply having many redundant sequences rather than fewer diverse sequences is likely to negatively impact contact prediction, and one would like to choose the optimal input alignment for this process.

In an effort to better estimate the robustness of the trees which were generated, bootstrapping [32] was also performed (N = 1000), in which variants of the input alignment are used to create trees which are compared to the initial tree.

As a control, multiple sequence alignment blocks were shuffled using a randomization algorithm that takes care not to introduce randomization artifacts and produces random alignments of the same length, base composition, overall conservation, local conservation pattern, and gap pattern as the input alignment [44].

Input alignment file was generated using MUSCLE.

The parallel I/O to read in the input alignment is optimized in two ways.

Lastly, we implement a novel method for calculating locally collinear subgraphs from the input alignment graph.

A phylogenetic tree is only as good as the input alignment.