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The Gamma mixture program
This program calculates the likelihood of a tree and the evolutionary rate for each site in a protein sequence alignment using the Gamma mixture model.
Source code and copyrights:
download the Windows executable: [gammaMixture.exe]
Source code (C++) for UNIX and LINUX is also available for download here: [gammaMixtureSrc.zip].
To compile type: g++ -o gammaMixture.exe -O3 *.cpp.

seq.aln (Clustal file format).
tree.txt (Newick tree file format).

You can try the program by typing
gammaMixture.exe -s seqFile -t treefile -c 2
seqFile is the input alignment file, treefile is the assumed phylogeny (newick format) and the -c  flag specifies the number of gamma components (in this case 2)
To get some more help you can use the -h flag ("gammaMixture.exe -h ")


In citing the Gamma mixture model please refer to:

Mayrose I, Fridman N, Pupko T. 2005. A Gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics. 21: Suppl 2:ii151-ii158.

Usage:

Flag Description Default
-s [MSA file] The input sequence file name.
The following formats are supported: Mase, Molphy, Phylip, Clustal, Fasta 		Obligatory
-t [tree file] The input tree file name (in Newick format) An NJ tree is constructed
-o [output file] The results output file r4s.res
-a [sequence name] Reference sequence name in the MSA. The conservation scores are printed based on the amino-acids in this sequence. First sequence in the MSA
-c [number of gamma components] specifies the number of gamma components (distributions) to fit 1b
-k [categories number] The number of discrete categories per Gamma component 16
-m [evolutionary model] The following amino-acids models are supported:
DAY (-md), JTT (-mj), REV (-mr), aaJC (-ma).
 -mj
-b [branch-lengths optimization] Branch lengths optimization flag:
-bn = no Branch lengths optimization
-bg = optimization using the Gamma mixture model 		-bg -h help