There is open source software to do this.
Any references you could share?
However if you have the boards made I strongly suggest to let the PCB manufacturer deal with panelisation. They can do it quicker & better than you.
No doubt, they can do it quicker and better... but for whom - me or themself?!
In past, I throwed some designs to PCB fabs and asked from simple "just here a few boards, do what ever you think is right" and detailed one - "back and forward list of requirements and optimization". Usually, worked on 50/50 basis, sometimes I thought what on hell they're thinking or a time overhead so enormous to be involved, another extreme - brilliant job.
Overall, that's depends from PCB fab expertise and to be tied to a single place is not option, but each PCB fab has same machinery...
Since then, I do panel prep gerber in house, works for me.