GAME

GAME is a program that computes the optimal value of the gamma shape parameter (alpha*) as described in Guindon and Gascuel (2002). This is a fast distance method based one fastME (Desper and Gascuel, 2002), which allows very large data sets (up to 1000 taxa) to be dealt with using a standard PC.

This page contains GAME executables for Windows, Linux, SunOS and Mac OSX and C source codes. The main option is to deal with DNA or protein sequences alignments. In this case, data sets can be analyzed under several substitution models (JC69, K2P, TN93 for nucleotides and JTT for amino acids). This option allows to find alpha* and the corresponding tree for one or several data sets (as generated with SEQBOOT for example). GAME can also compute the value of alpha* from a serie of distance matrices. This option is limited to a unique data set.


	Efficient biased estimation of evolutionary distances when substitution rates vary across sites (see Stéphane Guindon and Olivier Gascuel, 2002 ) Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle. (see Richard Desper and Olivier Gascuel, 2002)


	References Felsenstein, J. (1989). PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics . 5:164-166 Guindon, S. and Gascuel, O. (2002). Efficient Biased Estimation of Evolutionary Distances when substitution rates vary across sites. Mol. Biol. Evol . 19:534-543. Gascuel, O. 1997. (BIONJ). An Improved Version of the NJ Algorithm Based on a Simple Model of Sequence Data. Mol. Biol. Evol. 14:685-695 Desper, R., Gascuel, O. (2002). Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle. Journal of Computational Biology 19:687-705