A new version of the program is available.
The branch and bound algorithm is now intergrated in the FASTML program.

FASTML version 2.02


Supplementary information of the paper: 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.

Pupko, T., Pe'er, I., Graur, D. Hasegawa, M., and Friedman N. 2002. Bioinformatics 18(8): 1116-1123. [pdf] [abs]

e-mail: talp@post.tau.ac.il
Tel: 972-3-640-7693
Fax: 972-3-642-2046

Abbreviations: Lysozyme ( Lys); Cytochrome oxidase subunit 1 (Co1); Cytochrome oxidase subunit 2 (Co2); Steroid receptor: (Steroid).

Sequences alignments (clustal format): Lys,  Co1, Co2, Opsin, Steroid

Tree topologies (treeview format).

Under the homogenous model: Lys, Co1, Co2, Opsin, Steroid.

Under the Gamma model: Lys, Co1, Co2, Opsin, Steroid.

Program:

Download the program (bnb.exe, version 1.01, PC executable)

Usage: the program is used with the following command line argument (i.e. bnb.exe commandLineArgumentList)

Command line (explanation, example)