Comparative genomics

TREECON

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between these distance values. In pairwise distance methods, the dissimilarity (fraction of substitutions) is usually converted into evolutionary distance by correcting for multiple mutations.

ASaturA

The usual way to demonstrate saturation in nucleotide sequences is to plot the fraction of differences between sequences against the evolutionary distance separating them. When the number of observed differences, for example for the fraction of third codon positions, no longer increases with increasing evolutionary distance, the sequence is said to be saturated. The same technique can be applied to amino acid (aa) sequences. We have developed a Java application called ASaturA that discriminates aa substitutions with high and low probabilities of occurrence.

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