FASTML is a program for computing the ancestral amino-acid sequences of a phylogenetic tree.
Current version is from 22.12.2011.
For support and questions please email me:

The program is now available as a web server at:
Source code, help on usage and executables for Windows can also be found there.



1. Pupko, T., Pe'er, I., Graur, D. Hasegawa, M., and Friedman N. 2002. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics 18(8): 1116-1123. [pdf] [abs]

2. Pupko, T., I. Pe'er., R. Shamir, and D. Graur. 2000. A fast algorithm for joint reconstruction of ancestral amino-acid sequences. Mol. Biol. Evol. 17(6): 890-896. [pdf] [abs]

3. Pupko, T. and Pe'er I. 2000. Maximum likelihood reconstruction of ancestral amino-acid sequences. Currents in Computational Molecular Biology. Ed. Miyano, S., Shamir, R, and Takagi, T. pp. 184-185. Universal Academy Press, Tokyo, Japan. [pdf]

Here you can find an older version of the program:
FASTML (version 2.02): fastml.exe (version 2.02)
FASTML (version 1.05): FASTML version 1.05
Branch and bound program (version 1.01): bnb version 1.01