Sentence examples for model for nucleotides from inspiring English sources
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.
The species tree was inferred under the coalescent model from the 248 individual ML gene trees obtained by PHYML with SPR moves on a BIONJ starting tree under the GTR + G8 model for nucleotides and the LG + G8 model for amino acids.
Phylogenetic analysis of the sequences from the partial L gene and the complete N gene was carried out with MEGA 3 program (22 ) by using the Kimura 2 parameter model for nucleotides and amino model with Poisson correction for amino acids to calculate distances between sequences with confidence values of 1,000 bootstrapping trials.
Open image in new window Figure 6 Model for nucleotide-induced NBD dimerization of the K ATP channel.
We used the HKY model for nucleotide sequence analysis and the JTT model for amino-acid sequences analysis.
Distance matrixes were generated using the Tamura Nei model for nucleotide and PAM model for amino acid using the MEGA 4.0 program [13].
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.
