Could someone direct me to a resource (textbook chapter, lecture notes, online video, etc.) that demonstrates, in a mathematically or computationally rigorous way, how to use maximum likelihood estimation to generate a phylogenetic tree, given a set of aligned sequences?
I've found several resources which describe the procedure for maximum likelihood estimation, such as giving the formula and the parameters that need to be determined (which I already know) and how to use it for aligned sequences (I already know this), but I really would like a worked-out example so that I can confirm my own mathematical thought process and make sure I am doing it right. I can't find anywhere that shows me how to do it from beginning (start with nothing but sequence alignments) to end (arrive at a tree).
Alternatively, if someone is willing to work out a small example, how would you use maximum likelihood estimation to generate a tree for the following three sequences?
organism_1 ATCG
organism_2 ATCC
organism_3 ATTT
