Estimation of the Expected Number of Substitutions at each Amino Acid (Nucleotide) Site and the Parameter for Rate Variation among Sites. GZ-gamma estimate the expected number of substitutions of each amino acid (nucleotide) site, and the gamma shape parameter for the rate variation among sites, using a combination of ancestral sequence inference and maximum likelihood estimation when the phylogenetic relationships of these homologous sequences are known.

This package contains two programs: gz-aa.exe for amino acid sequences, and gz-DNA.exe for DNA sequences, which are encoded in C language. To use the program, you need one input file containing the amino acid (or nucleotide) sequences and the tree topology of these sequences (see atp6.aa for an example). This file begins with two numbers: the number of sequences and the number of amino acid or nucleotide sites (sequence length).

The second line will be the name of the first sequence, and the third line will be the first sequence, and so on. Each sequence should occupy a line without any interruption. Only the letters (capitalized) for the 20 amino acids (or 4 nucleotides) are allowed in the sequences. The gaps or any other symbols should have been already removed. The last line of the file is the tree topology of the sequences.
The tree format is the same as that used in PHYLIP package. Note that the tree is unrooted, so trification rather than bification is required for the deepest branching node

The license of this software is Freeware, you can free download and free use this calculator software.