Not being a geneticist I can’t comment on it in detail, but here are one or two observations anyway.
My first impression is that it’s not an easy article to understand. It uses a lot of technical terms that are unfamiliar to non-geneticists, and it doesn’t define them all that clearly. I’ve found this with other articles on creation.com as well – they tend to get a bit tough going when you try to follow them through and drill down into the details.
Secondly, it mentions that the author wrote a Perl script, but the script itself isn’t provided, so it’s not possible to review it for correctness. Having said that, it turns out that it’s quite common for scientific papers in mainstream journals not to include source code – a fact that those of us in the software development industry find quite astonishing, given that open source collaboration on GitHub is pretty much the lifeblood of computer programming these days, and that the correctness of computer code can make or break your conclusions.
It also mentions a computer program called Mendel’s Accountant, but it doesn’t explain clearly what it does. It turns out that it’s some kind of evolution simulator written by a team of YECs. The footnote links to a paper in a mainstream peer reviewed journal referred to as simply SCPE. Turns out that SCPE stands for “Scalable Computing: Practice and Experience” – in other words, it’s a journal about research into techniques for building high performance web applications.
Mendel’s Accountant is open source after a fashion – you can download it here. It probably needs a geneticist with programming experience to look at it and see what to make of it.