Character-based method= Look at the actual DNA letters (A, T, G, C). Use these aligned sequences to build a tree based on shared character
-Maximum Parsimony SLOW: Pohon terbaik = yang butuh paling sedikit perubahan. Calculates branch order - not branch length, Uses only “informational” positions, Tree with shortest total branch length = most parsimonious tree
-Maximum Likelihood SLOW= yang punya probabilitas tertinggi menghasilkan data kita, Multiple result trees are possible
-Bayesian= Gunakan data + informasi sebelumnya → cari pohon dengan kemungkinan tertinggi.