Sentence examples for using the nucleotide alignment from inspiring English sources

Using the nucleotide alignment, hierarchical likelihood ratio tests indicated that the Tamura 3-parameter + Γ (with a = 1.24) model was the most appropriate model of DNA sequence evolution.

We inferred a Bayesian phylogenetic tree (Huelsenbeck and Ronquist 2001) for each of the 5,282 E. coli and Shigella gene families (N > 4) using the nucleotide alignments, then aggregated all strongly supported bipartitions (PP ≥ 0.95) using matrix representation with parsimony (MRP) (Ragan 1992) to generate a E. coli– Shigella supertree.

To assess whether viruses in lung evolve differentially from those in blood, we used the nucleotide alignments to calculate two statistics: (1) divergence, which is the genetic distance between nucleotide sequences from blood and lung to the inferred MRCA (Figure 4); and (2) the mean pairwise nucleotide diversity of viruses in blood and lung samples (Figure S2).

Additionally, we used the nucleotide alignments of the beta-keratins in the three turtles and P. nelsoni to assess the phylogenetic relationships of these genes in Chelonians.

To ensure the high accuracy of the results obtained using the nucleotide sequence alignment tools, an e-value of less than 10-5 and a maximum identity of equal to or higher than 98% were considered for the correct identification of Candida at the species level.

Multiple alignments of the nucleotide sequences of the 7 housekeeping genes (gyrB, atpD, dnaK, efp, groEL, glnA, recA) for the 11 taxons were performed using ClustalW (The nucleotide alignment is provided in Additional file 6).

Assembled contigs were searched for viral sequence by comparison to the nonredundant nucleotide database in Genbank (downloaded March 2013) by using the nucleotide basic local alignment search tool (National Center for Biotechnology Information, Bethesda, MD, USA).

Each primer and amplicon sequence was tested using the nucleotide-nucleotide BLAST alignment tool to ensure minimal similarity with any other sequence.

The protein sequences of orthologous genes were aligned using muscle (Edgar 2004), and the protein sequence alignment was then used to construct the nucleotide alignment.

Then the aligned amino acid sequences were used to construct the nucleotide alignment.

The t inference was performed under the Bayesian phylogenetic framework, implemented in BEAST 1.7.4 [ 87], by using the pol nucleotide alignment that was used in the phylogenetic reconstruction.