Phylogenetic molecular clock

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. 

Doolittle WF (1998) You are what you eat a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14 307-311 Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284 2124-2129 Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution does a relaxed molecular clock reconcile proteins and fossils Proc Natl Acad Sci USA 101 15386-15391... 

Takezaki, N., Rzhetsky, A. and Nei, M. (1995) Phylogenetic test of the molecular clock and linearized tree . Molecular Biology and Evolution, 12, 823-33. 

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