I have constructed phylogenetic tree using NJ method in ClustalX and ML in PhyML. I also mapped my protein sequences belonging to NCBI taxons to the tree of life. Now I am wondering how to interpret the difference in tree structure obtained using these two methods.
Comparing a species tree (taxonomic) and a gene tree is something interesting. You would find a lot of informations and paper by looking up "species and gene tree reconciliation" methods. Another important explanation not mentioned by Heng is horizontal transfer of genes, and comparing both trees is a way to detect such an event.