GZ-Gamma Estimation of the Expected Number of Substitutions at each Amino Acid Site
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GZ-Gamma Ranking & Summary

GZ-Gamma Tags

sequence estimation acid DNA sequence Time estimation Acid Titration DNA acid font disparity estimation ACID transaction FDR estimation find amino acid amino acid finder search amino acid Amino Acid analyzer amino acid sequence amino acid amino acid translator extract amino acid performance estimation osmosis estimation acid solution amino acid residue optimal amino acid analyze amino acid nucleic acid count substitutions number analyze amino acids pair amino acids pair analysis large phylogeny estimation amino acid sequence analysis analyze amino acid sequence amino acid classification Amino Acid Topology AminoAcid Analysis Phylogenetic Relationship AminoAcid amino-acid detector detect amino-acid effort estimation analyze amino acid chain acid loops expected expected return acid pro acid pro 7

GZ-Gamma Description

GZ-gamma was developed to 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

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