Sentence examples for distance substitution from inspiring English sources
To determine the best tree-building method, several algorithms were chosen including maximum likelihood, neighbor-joining using the Kimura-2 distance substitution model (data not shown) and neighbor joining with uncorrected distances using PAUP* 4.0b10 [104].
Neighbor-joining phylogenies used an amino-acid percentage distance substitution model and 1,000 bootstrap reiterations.
We observed a high degree of genetic conservation in terms of evolutionary distance (substitutions per site) within the Canadian whole-genome data set, which is in keeping with A/H1N1pdm virus emerging within an immune-naïve population.
Genetic distance (substitutions per nucleotide position) and neighbour-joining tree inferred from myxobacterial 16S rRNA gene sequences.
Genetic diversity was calculated as the mean pairwise distance (substitutions per site) using the Maximum Composite Likelihood method 23 in MEGA5 24; the P values were calculated using an unpaired two-tailed Student's t test.
Neighbor-joining trees building and bootstrapping were carried out with Mega 3.1 [ 23] using 1000 bootstrap replications and p-distance substitution model.
Multiple sequence alignment (MSA) was carried out with CLUSTALW 1.83 [ 22]; neighbor-joining trees with bootstrap were inferred by Mega 3.1 [ 23] with 1000 bootstrap replications and p-distance substitution model.
The unrooted phylogenetic trees were generated by the neighbour-joining (NJ) method using ClustalX and with the p-distance substitution model in MEGA 4. Bootstrap analysis was performed with 1000 replicates to obtain a support value for each branch.
The phylogenetic trees were reconstructed with MEGA v4.0 [ 48] using the Minimum Evolution (ME) and Neighbor-joining (NJ) methods with the parameters of pairwise deletion of gaps/missing data and the p-distance substitution model where only the transversions were taken into account.
To obtain a measure of the divergence of the sequenced myxobacterial genomes, the 16S rRNA genes of each genome were aligned and distances (substitution frequencies per nucleotide) between each pair of sequences calculated, allowing construction of a phylogenetic tree (see Methods).
This relationship between LCR distance and substitution is also apparent for substitutions segregating within humans, as shown using the data from the 1000 Genomes Project.
