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.

If there are problems with the compilations (occasionally, with old version of g++) - please email me and I'll try to help. To modify the code, or use parts of it for other purposes, permission is requested. Please contact Tal Pupko at


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