The marginal reconstruction method can be found in:
Koshi, J. M., and Goldstein, R. A. (1996). Probabilistic reconstruction of ancestral protein sequences. J Mol Evol 42, 313-320.
The joint reconstruction method can be found in:
Pupko, T., Pe'er, I., Shamir, R., and Graur, D. (2000). A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol 17, 890-896.