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Therefore, a nonstationary model should be used with parameters changing along with the explanatory variables.
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For single- and eight-channel data, the proposed dereverberation technique was used with parameters: D=9, α=5, β=0.05, a=0.005, and b=0.6.
A general time reversible (GTR) model with four rate categories and a proportion of invariable sites was used, with parameters estimated from the data.
TopHat-fusion [ 81] (v2.0.12) was used with parameters --fusion-search --fusion-min-dist 100,000.
Firstly, BLASTCLUST [ 24] was used with parameters: S = 80, L = 0.5, W = 16 to calculate the sequence similarity of the tRNA members.
To identify the stretches of the repetitive units, the REPUTER program was used with parameters -f –p –r –c –l 30 –h 3 –s and the repeat patterns along with the corresponding genomic co-ordinates were tabulated [ 81].
TMHMM2 [ 43], TmPred [ 44], and TopPred [ 45] were used (with parameters set to default values) to predict the number of transmembrane helices in the putative methyl-accepting chemotaxis proteins.
GapCloser was used with parameter '-p 31'.
Fourth, ab initio self-training gene prediction method GeneMark-ES [ 71] was used with parameter "--min_contig 10000".
Velvet algorithm was used with parameter hash length of 31, insert length of 250 and minimum contig length 50.
The PASW CS General Linear Model was used with parameter estimates of the separate effect of each predictor and Wald F statistics for the effects of child, parent, and teacher characteristics on the model.
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