To keep it short and simple, here are the rules of creating and commanding clans.
The key difference between just having a clan and having a bloodline is that with just a bloodline it is special to you and you alone. With a clan, other people old and new on the site can have your bloodlline. Once you become capable you can always turn your bloodline into a clan, though there will be a limited number of five to 7 clans allowed at once. When one set dies out, another will be allowed to be made. To create a clan, three people of a least A-rank to "back you up" One of the members will make an application, and the other two members will post they are also in the clan. An admin or mod will review and accept or deny the application. In the application, a village must be decided on for the clan, this clan cannot move villages. It will remain in that village until it dies out, or the village is destroyed. If the village hosting a clan is destroyed, different members can branch off and go to different villages. That of course is should those villages accept you, this is the only scenario where once a clan village has been decided on, any new apps holding that clan can be somewhere else besides that specific place. The makers of the clan are the heads, they decide just about every decision pertaining to the clan. If they don't want their ninja to go on missions, they won't and so on. The only way a leader can be replaced is if they step down, die or one of the conditions met for taking control of the clan is met.