Phylogenetic analysis, molecular

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Bohlmann J., Meyer-Gauen G. and Croteau R. (1998) Plant terpenoid synthases molecular biology and phylogenetic analysis. Proc. Natl. Acad. Sci. USA 95, 4126-4133. Boppre M. (1984) Chemically mediated interactions between butterflies. In The Biology of Butterflies, eds R. I. Vane-Wright and P. R. Ackery, pp. 259-275. Princeton University Press, Princeton, NJ. 

The home page of WebPhylip consists of three windows. The left window is the command window for selecting and issuing the execution (Run) of the analysis/ operation. The analysis results appear in the upper window. The lower window is the query window with options, a query box for pasting the query sequences (in Phylip format), and Submit/Clear buttons. To perform phylogenetic analysis, select DNA/Protein for Phylogeny method in the left window to open the available analytical methods (parsimony, parsimony + branch bound, compatibility, maximum likelihood, and maximum likelihood with molecular clock for DNA whereas only parsimony for protein). Click Run (under the desired method) to open the query window with options. Select the appropriate Input type (either interleaved or sequential), paste the query sequences and click the Submit button. The analytical results are displayed in the upper window (Figure 13.4). 

Retrieve the amino acid sequences of liver alcohol dehydrogenase from six organisms to perform phylogenetic analysis. Compare phylogenetic results from Fitch-Margoliash methods without (Fitch) versus with (Kisch) molecular clock using the Dayhoff PAM 001 matrix. 

Blastocystis hominis is a unicellular anaerobic organism that inhabits the human intestinal tract, and whose metabolism and life cycle are not completely understood. Molecular phylogenetic analysis of the SSU rRNA sequences (Silberman et al. 1996) and protein-coding sequences (Arisue et al. 2002c) show Blastocystis branching within stramenopiles (heterokonts), a group containing a vast diversity of photosynthetic and heterotrophic protists (Fig. 10.2). 

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