All free model parameters were estimated by RAxML where we used a GAMMA model of rate heterogeneity and ML estimate of alpha-parameter.
RAxML was used to generate a maximum likelihood phylogenetic tree with the GAMMA model of rate heterogeneity and LG empirical base frequencies (-m PROTGAMMAAUTO) and using 100 rapid bootstraps73.
We compiled the concatenated protein alignments created by PhyloSift to create maximum likelihood phylogenetic trees using RAxML v.7.2.861 using the "rapid bootstrap" method with 100 bootstraps and the "PROTGAMMAAUTO" model of rate heterogeneity.
The best partitioning scheme comprised two subsets, one (55,892 bp) evolving under the generalized time-reversible model of evolution with gamma model of rate heterogeneity and invariant sites (GTR+I+Γ) and the other (62,184 bp) under the GTR+I model.
As a footnote, while high-yield bond rates have been plummeting, preferred yields have been a model of rate stability.
The matrix was partitioned (i.e., ITS vs. rpL16 intron) with a gamma model of rate heterogeneity and proportion of invariable sites estimated by the program.
The formulation of RCM is carried out, considering the design challenges and the execution model of rate controlling factor in future Internet architecture.
Therefore, we also studied mutational saturation under a model of rate variation between synonymous sites.
All free model parameters were estimated by RA×ML using the GAMMA+P-Invar model of rate heterogeneity with an ML estimate of the alpha-parameter.
The uncorrelated Bayesian model of rate change implemented in BEAST ver. 1.4.4 [13] was used to estimate divergence times and to determine rates.
The methods described above were compared with two existing dating methods: penalized likelihood and an uncorrelated Bayesian model of rate change.
