I am aware of the pedigree and kinship2 libraries in R, but functionality is limited. Programs like EASYPOP can save pedigree information but are not focused on simulation of pedigree parameters specifically. I am interested in looking at e.g. the impact of founder inbreeding levels (usually assumed to be zero) on kinship estimates in subsequent generations.
I am just asking before trying to do something from scratch. :)
In R I don't know. In Fortran, Jack Windig have one which is available on demand (Windig and Oldenbroek 2015), and I personally must have some script somewhere. Depend on how specific is your demand :) ...
Use Vortex. You can use your pmx files as input and also provide microsatellite data. We did some simulations assuming different founder assumtions. Worked quite well.
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