Sentence examples for alignments were analyzed for from inspiring English sources

The multiple alignments were analyzed for alignment depth.

For each gene, a set of 200 simulated alignments was analyzed for positive selection using the same tests as in the original analyses.

Furthermore all mutations between the alignments are analyzed for their synonymous or non-synonymous nature, permitting the calculation of synonymous and non-synonymous substitution rates (Ks and Ka, respectively).

The 89 IHHNV capsid sequence alignment was analyzed for evidence of recombination breakpoints using the Genetic Algorithms for Recombination Detection (GARD) tool [36].

The alignment was analyzed for conservation using Kalignvu.

Each alignment was analyzed for single-nucleotide polymorphisms (SNP) using GATK [ 29].

The alignment was analyzed for recombination by Recco [ 41] with the Hamming mutation cost matrix and gap extension costs of 0.2.

Concatenated alignments were analyzed and used for tree construction by the same methods as described earlier.

Alignments were analyzed using standard configurations for the different methods with a 0.005 cutoff for the Bonferroni-corrected p-value.

Since phylogeny-based methods of detecting positive selection do not take into consideration the effects of recombination on sequence evolution, gene alignments were analyzed using GARD (Genetic Algorithms for Recombination Detection) to estimate recombining breakage points [ 27, 28].

Trees from MrBayes and sequence alignments were analyzed in PAML [ 49, 50] to test for evidence of selection acting on sites in the alignments.