FASTML (VERSION 2.02)
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: talp@post.tau.ac.il
The program is now available as a web server at: http://fastml.tau.ac.il
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
talp@post.tau.ac.il
References:
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