Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of phylogenetic trees with a fixed set of labels on leaves is not Euclidean, we cannot simply apply tools in data science. In this paper we survey some new developments of machine learning models using tropical geometry to analyze a set of phylogenetic trees over a tree space.