Converge Convergent and Parallel Evolution at the Amino Acid Sequence Level
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Converge Description

This application was developed to test convergent and parallel evolution at the amino acid sequence level. It computes the probabilities that the observed convergent and parallel substitutions are attributable to random chance. This package contains one program: converg2.exe, which is written in C language. To use the program, you need a input file containing the amino acid sequences and the tree topology of these sequences (see lysozyme.aa for an example). This file begins with two numbers: the number of sequences and the number of amino acid 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. Only the one letter code (capitalized) for the 20 amino acids are allowed in the sequences. The sequences should be aligned and gaps or any other symbols be removed already. 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 (Felsenstein 1995). Note that the tree is unrooted, so trification rather than bification is required for the deepest branching node.

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