Sentence examples for model for nucleotide from inspiring English sources

We used the HKY model for nucleotide sequence analysis and the JTT model for amino-acid sequences analysis.

PhastCons uses genome alignments of 17 species and a continuous-time Markov model for nucleotide substitutions and a two state phylo-HMM model to compute posterior conservation probabilities.

The DNADIST program of the PHYLIP package, using the Jukes-Cantor model for nucleotide substitution was used to generate the distance matrix analyzed by LIBSHUFF.

Distance matrixes were generated using the Tamura Nei model for nucleotide and PAM model for amino acid using the MEGA 4.0 program [13].

Arlequin 3.11 [53] was used to estimate genetic distances utilizing the phylogenetic relationship defined by 429 FASTA-formatted mtDNA haplotypes, assuming Tamura and Nei's [54] model for nucleotide substitution.

With the fishing cat as outgroup, we constructed phylogenetic trees using the software PAUP* (version 4.0) [25] and the best-fit model for nucleotide frequencies, transition-transversion ratio and nucleotide substitution by the Akaike Information Criterion (AIC) [26] in ModelTest (version 3.8) [28], [28].

Open image in new window Figure 6 Model for nucleotide-induced NBD dimerization of the K ATP channel.

As in the BEAST analyses, we employed the WAG model for proteins and the GTR model for nucleotides.

ML analyses were performed using Garli [ 72] with a GTR + I + G model for nucleotides and the WAG model for amino acids.

We produced a neighbour-joining tree of all alleles, including published DRB and DQB alleles from rat, mouse and human (Maximum Composite Likelihood model for nucleotides, 10000 iterations, starting seed: 90572, excluding deletions and allowing for heterogeneous patterns among lineages).

The Maximum-Likelihood (ML) phylogenetic tree was constructed in PHYML [ 83], under the best-fit model for nucleotides and amino acids, 1000 bootstrap replicates and the NNI branch search algorithm.