Phylogeny analyses

Sukhdeo et al. (1997) presented an analysis of the phylogeny of strongylid nematodes which they claim demonstrated that the ancestral nematode was a skin-penetrating tissue migrator, and that one clade of parasites (the Trichostrongylidae and Heligmosomidae) has secondarily... 

Beckenbach, K., Blaxter, M.L. and Webster, J.M. (1999) Phylogeny of Bursaphelenchus species derived from analysis of ribosomal internal transcribed spacer DNA sequences. Nematology 1, 539-548. 

Casiraghi, M., Anderson, T.J.C., Bandi, C., Bazzocchi, C. and Genchi, C. (2001) A phylogenetic analysis of filarial nematodes comparison with the phylogeny of Wolbachia endosymbionts. Parasitology (in press). 

Felsenstein, J. (1996). Inferring phylogenies from protein sequences by parsimony, distance and Likelihood methods. In Computer Methods for Macromolecular Sequence Analysis (Doolittle, R. F., ed.), Methods Enzymol. 266, 418-427. 

Maddison, W. P, and Maddison, D. R. (1989). Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol. 53, 190-202. 

Fig. 1.11. Phylogeny of the Aspidogastrea at the family level, according to a reanalysis of characters in Gibson (1987) by Brooks etal. (1989) and recently from a broader analysis by Zamparo and Brooks (2003) figures of animals redrawn from Rohde (2001).

Fig. 5.2. Phylogeny of monopisthocotylean Monogenea based on SSU rDNA. The tree topology is from a Bayesian analysis with nodal support indicated, from top to bottom, for maximum likelihood (bootstrap%, n = 100), maximum parsimony (bootstrap%, n = 1000) and Bayesian inference (posterior probabilities). Figure from Matejusova etal. (2003).

Ghiselin, M. T., Summary of our current knowledge of metazoan phylogeny, in The hierarchy of life molecules and morphology in phylogenetic analysis, Fernholm, B., Bremer, K., and Jomvall, H., Eds., Exerpta Medica, Amsterdam, 1989, 261. 

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 nucleotide sequences encoding type C lysozyme precursors from eight organisms and draw their phylogenies of the consensus tree after performing compatibility analysis at WebPhilip. 

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