*Note: * The first version of ProtTest contained an implementation of the Nearest-Neighbor-Interchange (NNI) algorithm. This algorithm proved to be too slow and inaccurate compared to the Minimum Evolution algorithm (ME), the latter was modified and made the default.
A fundamental assumption was made regarding the evolutionary pattern of the sequences being analyzed: The rates of evolution among sequences are assumed to follow an equal branch rate model. In this model, the ratio of 0531ecd6aa
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