Phylogenetic analysis of biosequences

A variety of methodological difficulties accompany different tree-making algorithms. Variation of mutational rate patterns among sites and lineages, multiple and relromutation events, functionally constrained sites and ancient evolutionary events make the estimates of distances uncertain. The assumptions and approximations in assessing evolutionary distances make estimates less reliable as sequence similarity diminishes. 

Losses in phylogenetic information may arise from mutation saturation, lateral gene transfer and a reconstruction artifact, long branch attraction phenomenon (Brown and Doolittle, 1997 Philippe and Laurent, 1998). 

Different phylogenetic reconstructions may result for the same set of organisms based on analysis of different proteins, genes or noncoding sequences. 

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Figure 18.1 Flow chart for phylogenetic analysis of biosequences...

The universal tree of life represents a hierarchical phylogenetic classification of the living organisms based on comparative analysis of biosequences encoding rRNA and several proteins (Doolittle, 1999). The two major problems with inferring phytogenies from biosequences are ... 

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