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Thereafter, the sequence data were fitted to the topology of the main supertree under the optimal evolutionary model (see Additional file 6; and [ 125, 126]) using PAUP* and the Perl script seqFitter.pl v1.0.
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Modeltest was used to determine the optimal evolutionary model for the dataset [48].
The optimal evolutionary model for the family was calculated from this alignment with ProtTest [ 64].
The optimal evolutionary model was GTR+I+Γ, both for the combined data and the individual gene fragments.
The optimal evolutionary model was selected for each gene based upon the Akaike information criterion (corrected) ranking implemented in jModelTest.
ModelTest [ 45] was used to select the optimal evolutionary model for each dataset, based on hierarchical likelihood ratio tests.
These software search for an optimal evolutionary scenario for the association between hosts and their symbionts (for example, parasites).
In searching for the optimal solution, evolutionary theory assumes a space of possibilities.
under the optimal training is given by (27).
The maximum DH (35.13%) was obtained under the optimal conditions.
To identify the optimal parameters, the evolutionary parameter optimization shown as Equation 7 in Methods was performed [ 21, 22].
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