For a course project, I should go through this paper: "A Poissonian Model of Indel Rate Variation for Phylogenetic Tree Inference" and fully understand this. I have a shallow background on phylogeny trees and HMM, and have serious problem in understanding the paper. I have tried to understand the referenced papers too but I was unsuccessful.

Is there any book discussing similar material that I can use to increase my background knowledge? What is your general suggestion?

Thanks.