MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known.
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P.-A. Christin, G. Besnard, E. Samaratini, M.R. Duvall, T.R. Hodkinson, V. Savolainen and N. Salamin. (2008).
Oligocene CO2 decline promoted C4 photosynthesis in grasses.
Current Biology 18: 37-48