Consensus tree

Fig. 6.1 Interrelationships of chemoreceptors internal (neurotransmitters) and external chemosignals. Phylogenetic connections for sequences in transmembrane (Fig. 6.2) domains Nos. = bootstrap values from 100 Megaline searches (based on majority consensus tree). Invertebrate — DrOR fruit-fly, CeOR nematode vertebrate — FOR fish, LOR (1 2) lamprey, MOR mouse VR (1 2) vomeronasal (from Dryer and Berghard, 1999).

Consensus tree Consensus DNA/Protein Compute consensus tree by majority rule... 

Select Do Consensus and click Run of Consensus tree (left window) to open the request form (lower window). Choose Yes to Use tree file from last stage and click the Submit button to display the consensus tree (upper window) and save the tree file. Select Draw trees and click Run of cladograms/phenograms/phylogenies. Choose Yes to Use tree file from last stage and click the Submit button to save the drawing treename.ps. 

The amino acid sequences for cytochrome C are given below. Draw clado-gram of the consensus tree after conducting parsimony analysis at WebPhylip. 

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. 

The DNA nucleotide sequences encoding tRNA specific for phenylalanine are given below. Draw a cladogram of the consensus tree after performing parsimony analysis + branch bound at WebPhylip. 

Retrieve the amino acid sequences of type C lysozymes from twelve biological sources. Perform ClustalW multiple sequence alignment and WebPhylip parsimony analysis to draw a cladogram of the consensus tree. 

Repeat resampling 1000 times compute majority-rule consensus tree i... 

Applicability Domain for DT-Based Models We describe applicability domain for QSAR models as being determined by two parameters (1) prediction confidence, or the certainty of a prediction for an unknown chemical, and (2) domain extrapolation, or the prediction accuracy of an unknown chemical that lies beyond the chemical space of the training set [60]. Both parameters can be quantitatively estimated in the consensus tree approaches, where individual models are constructed as DTs. Taken together, prediction confidence and domain extrapolation assess the applicability domain of a model for each prediction. 

A model s limitations should be assessed from three different perspectives (1) overall model predictivity (model validation), (2) individual prediction confidence (applicability domain), and (3) chance correlation. These attributes can be more readily assessed in the consensus tree modeling such as the DF method than in other QSAR methods. Using DF as an example, we have found the following ... 

Restrepo, G. and Villaveces, J.L. (2005) From trees (dendrograms and consensus trees) to topology. Croat. Chem. Acta, 78, 275-281. 

Figure 3 Phylogenetic relationship of the Cordyceps fungi based on the total sequence data. A tandemly concatenated nuclear and mitochondrial rDNA data set (4272 nucleotide sites) was subjected to neighbor-joining (NJ), maximum-likelihood quartet puzzling (ML-PUZZLE) and maximum parsimony (MP) analyses. The strict consensus tree of the three analyses is presented. Numbers at the nodes are bootstrap values (%) obtained by the NJ (left), ML-PUZZLE (center), and MP (right) methods, respectively. Shown on the right side are host organisms, names of the clades, and morphological types of the stromata.

Abbreviations used CT, consensus trees/supertrees DC, distance calculation DM, distance matrix G, general I, invariant method ML, maximum likelihood P, parsimony, TM, tree manipulation. 

The strict consensus tree from these two trees (Fig. 4) showed three major clades (plastome groups A, B, and C) within the subgenus, each of which was supported by a large number of restriction site characters on the shortest trees. 

FIGURE 10.11 Pruned consensus tree for Heterandria and Xiphophorus, showing four nodes of agreement obtained by removing unique and conflicting area positions from the two reduced area cladograms shown in Figure 10.9. 

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