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They have a LOT written on that. Here is a place to start:
IMHO the basis is this. If your company is a large enterprise that does scaled agile, like SAFe, and therefore has several teams and organizations that all need to be coordinated and tracked, along with being managed from the portfolio level, then Jira Align is your solution! Particularly if you have several Jira instances that you want to manage things like dependencies across.
If you just have a set (5-10) of agile teams that need to be coordinated and have dependancies mapped between the teams, then Jira AR is the tool for you.
As far as what is available in Align that is not in Jira AR a whole lot. Portfolio management, 128 different reports, Program boards, work trees, enterprise level tools, and MUCH Much more.
How do you map across instances? I have two scenarios for this:
1. My company has acquired other companies who previously set up their own Jira instance. So not sure if there will be domain issues or some other adjustment to the account that needs to be made so JA knows this is now the same company.
2. Before my company officially started using Jira a number of teams setup their own free instances. Is there a way for those to now be recognized. Or for one small instance to coordinate with another small instance?
I am curious about these scenarios regarding using either Jira Advanced Roadmaps 'Plans' and Jira Align.