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To test the substitution matrices, we performed maximum likelihood calculations on each family of Table 2. Since the models compared have the same number of parameters, they can be compared using Maximum Likelihood (ML) values obtained using a reasonable phylogenetic tree topology [ 42, 43] (see Methods).
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In the first model, differences in the estimates for the same geographic area were compared using the maximum amount of overlap between adjacent surveys.
The goodness of fit between alternative models was compared using the maximum likelihood technique.
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To test for positive selection in individual codons of mammalian TLR sequences, the dN to dS ratios were compared using two maximum likelihood (ML) frameworks, the Hyphy package implemented in the Data Monkey Web Server (http://www.datamonkey.org[ 77] and the CODEML PAMLL version 4) [ 78] as proposed by Wlasiuk and Nachman (2010).
In this paper, the performances of different forecasting systems are compared using the daily maximum ozone levels across three locations in Kuwait.
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However, to evaluate the significance of interaction terms, models with and without interaction terms were compared using AIC values estimated with the maximum likelihood method.
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