Sentence examples for alignments were analyzed in from inspiring English sources

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

The multiple-sequence alignment was analyzed in JalView 2.10.1 and the first three bases of haplotype 2.1 were corrected to positions 24–26.

The alignment was analyzed in a Bayesian phylogenetic framework using MrBayes 3.1 [67].

The alignment was analyzed in ProtTest v. 2.3 to determine the most appropriate protein model for subsequent analysis [20].

Each pairwise nucleotide sequence alignment was analyzed in PAML [ 38] to estimate dN (average number of nonsynonymous changes per nonsynonymous site) and dS (average number of synonymous changes per synonymous site).

All amino acid sequence alignments were analyzed under parsimony in PAUP* version 4.10 (Altivec) [202].

All nucleotide sequence alignments were analyzed under maximum likelihood in PAUP*.

The nucleotide sequence alignments were analyzed by using MRBAYES 3.1.2 (12 ) in the computer software package PAUP*, version 4.0b10 (http://paup.csit.fsu.edu).

The global sequence alignments of the 11 EBV genomes and individual gene sequence alignments were analyzed using Kalign and Clustal Omega in EBI (http://www.ebi.ac.uk/Tools/msa/kalign/; http://www.ebi.ac.uk/Tools/msa/clustalo/) respectively.

The three alignments were analyzed with MrBayes 3.1.

The multiple alignments were analyzed for alignment depth.