Constructing Phylogenetic Tree And Analysing Evolution Of A Protein

Question

[Pappu]

I am trying to understand the evolution of a protein domain by constructing Phylogenetic tree and by analyzing its last common eukaryotic ancestor (LCEA). I obtained the homologs by blast search, then used Muscle for MSA and FastTree (since number of sequences is >1000, PhyML was too slow) to construct the phylogenetic tree. I am wondering if it is the right way to go. I am willing to know how to interpret the tree, find out the LCEA and explain how the protein has evolved. Thank you.