Migrate to new nomenclature

[manulera]

In the last nomenclature paper we have introduced some changes to the nomenclature, namely making the insertion, substitution and multiple substitution syntaxes all the same

• single substitution: A123V -> does not change
• multiple substitution: APL-123-VVV -> APL123VVV
• insertion: A123-VVV -> A123AVVV (putting the aminoacid after which the insertion happens before and after)

Required tasks:

• [x] #76 -> @kimrutherford
• [x] #78 -> @manulera
• [x] #79 -> @kimrutherford
• [x] #80 -> @manulera
• [x] #81 -> @manulera

[manulera]

I think we are done with this one @kimrutherford!