Sometimes I want to play with different Modeller options and parameters
while working with the same alignment file.
However, to avoid overwriting the previous results, I actually have to
modify the alignment file and Modeller script anyway by changing the
target sequence name.
Am I doing something wrong and is there a better way?
Right, this is the normal way that automodel names its output files. But
you can change this by subclassing and overriding the
get_model_filename() method: