in the subalignment [sequences were weighted using the same technique as in (1)], and used it to construct an initial model using the modelfromalign program in SAM3.1. We then used this initial model as input, in addition to the sequences themselves, to the buildmodel program using the same parameters as in (7). As a result, unlike in previous versions of PANTHER, the HMMs can have different lengths for different subfamilies, and now model any domains that are conserved across a single subfamily but not found in other subfamilies.
