A neighbor-joining bootstrap resampling analysis (1,000 replications) also was performed to assess support for specific nodes, again by using the ML substitution model.
However, distances calculated using the ML HKY85 model and estimated proportion of invariant sites puts Amborella-sister with low BS of 58% [see Additional file 5], while distances derived from the ML HKY85 model with four gamma-distributed rate categories estimated gives Amborella-sister with stronger support (89%; Fig. 3B).
Five trimmed data sets, in which the sites with the highest rates of sequence evolution were deleted by 5% increment, were analyzed using the ML (LG-Γ4 model) and BI (CAT + Γ4 and CATGTR + Γ4 models) methods.
Similarly, in our study, using the ML-TIRM model, the total width of the 95% confidence interval surrounding the estimate was 38% of the estimate when applied to the entire four years of data and 61% when using the 2007 data only.
The identified homologs were used to construct the phylogenetic trees using the ML, BI and NJ methods (substitution model: TrNef + I + G) implemented in the TOPALi program [53].
We found that the swine flu viruses are not clustered correctly by using the ML method with the J-C model (figure 4(a)) and the origin of A H1N1 virus is not clear by NJ method with Kimura model (figure 4(b)) since A H1N1 genomes are all very far away from other genomes.
For normalizing the variations in the glottal parameters of the children test set "CH1" with respect to those of the adults training set "TR1" used for training the acoustic models using the ML-based approach, the OQ, RQ, and SQ of the signals are modified by factors ranging from 0.55 to 1, 0.35 to 1, and 0.45 to 1, each with a step size of 0.05, respectively.
For all ML analyses we also calculated a NJ tree using distances calculated from the ML model being tested.
We use the Morris Lecar (ML) model [23] in the present study.
Alvarez-Valin et al. (2004) and Gu and Li (2006) used the ML method with the nonhomogeneous model (i.e., the "time-nonhomogeneous" Markov model) (Galtier and Gouy 1998) to reconstruct ancestral states and obtained the opposite conclusion from the "vanishing isochore" hypothesis at least in certain lineages.
