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The parameters A and α were estimated by maximum likelihood (see Methods section).
Retained individuals after all these procedures were assigned to their respective cluster, according to the K = 10 run with the maximum likelihood (see below Cluster analyses), if they had a coefficient of membership to that cluster equal or higher than 0.70.
The ratio of deletion to point mutation (represented by the slope) was estimated using maximum likelihood (see Materials and Methods).
Although c may be defined by a user, we suggest estimation by maximum likelihood (see the next section).
Phylogenetic analyses were conducted primarily using Bayesian methods, but major results were confirmed using maximum likelihood (see below).
Our requirement that three parameter optimizations produced model likelihoods within five log-likelihood units of the maximum likelihood (see Methods) greatly increased the computational burden associated with parameter optimization.
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We further explored the evolutionary history of Lac.2 by aligning the operon from each S. agalactiae isolate to 16 additional Streptococcus species representing a range of phylogenetic groups (mitis, sanguinis, mutans, pyogenic, and bovis) and then constructed a maximum likelihood phylogeny (see Methods, Figure 5, and Additional file 1).
In this section, after the general overview of the receiver structure in Section 4.1.1, we describe two different dual-stream multiantenna demodulators, namely a linear minimum mean squared error (MMSE) receiver (see Section 4.1.3) and an approximate maximum likelihood receiver (see Section 4.1.4) [22 24].
A comparison of the trees generated by the Neighbor-Joining method (see Additional file 5) and the Maximum Likelihood method (see Additional file 6) shows that generally the Maximum Likelihood has more conservative bootstrap values.
The phylogenetic relationship of the PKS N-terminal region among dinoflagellates is shown in a maximum likelihood phylogeny (see Additional file 2: Figure S5).
Coalescence time of the 21 major haplogroups of Tibetan highlanders was estimated employing ρ-statistic based method and maximum likelihood method (See details in Methods).
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