I have recently started this book "Bioinformatics and Functional Genomics" by Jonathan Pevsner which has really inspired myself to dive deeper into bioinformatics and become more familiar with the subject. However, my background is in biology not computational sciences although I have worked in a genomics laboratory and have had experience with manipulating data. I find myself stuck on the math portion of this book and cannot seem to follow along with the equations and the applications of them. I am not sure if their are just math concepts that I am missing or that I am just focused too much on the formulas and worrying about not getting the same result as the text. Does anyone have any recommends to supplement the math component of this book?

I remember talking to Jonathan on a teleconference a few years ago, but cannot remember for what, exactly. Is there are particular part at which you are stuck? I find that people can go years with particular 'uncertainties' in their head, which, when finally understood, can indirectly help the understanding of other things. I remember going years not perfectly understanding 'adjustments' in regression models, but now I get it since 2016.

Apart from what I've said, there is a wealth of material online. Why not just use a search engine to find blogs and tutorials to help the understanding?

Well I recently reached Chapter3 in his book on pair wise alignment of sequences and he goes on to explain the several steps of creating Margaret Dayhoff PAM matrices. I try to use his formulas to reconstruct the matrices and I just seem to get lost every time. He doesn't necessarily go into the math in great detail and other sources seem to use different formulas/different approaches.

It's certainly not one oft he main themes that we see here on the forums, reflecting the fact that not many people are working on this particular area. Have you tried a simple search engine?

I've found some useful material already: