More flexible sequence weight handling

[thomashopf]

Right now, sequence weights are done in a very rigid way - computed inside plmc, no option to export etc.

Ideally, we would be able to:

• export sequence weights computed by plmc, or - even better - move the computation to a dedicated step
• allow user-defined sequence weights or reuse existing weights
• have more elaborate sequence weighting schemes
• have faster sequence weighting algorithms instead of all vs all which becomes prohibitively expensive for large alignments