Bootstrapped trees

Figure 4.7 Consensus bootstrap tree of full-length amino acid sequences of insect desaturases generated with MacVector 7.0 (Oxford Molecular Limited). Branch points (internal nodes) are retained if they occur in >50 percent of resampling trees (1000 x resampling) all other nodes are collapsed. Names in bold are from the published literature names in parentheses reflect a nomenclature system for insect desaturases (proposed in Knipple ef a/.,...

Fig. 3. Minimum phylogenetic tree from tRNA sequences. The tRNA sequences from Fig. 2 were analyzed by a maximum parsimony algorithm. Organisms are abbreviated as in Fig. 2. The branch lengths are proportional to mutational distance and numbers above branches refer to the percentage of bootstrap trees which confirm that branch. is used to represent over 95%. Branches which are not confirmed to more than 50% are collapsed to the next nearest node.

Figure 9.7 50 per cent majority-rule consensus bootstrap trees based on the mitochondrial tRNA data set using the lamprey as outgroup. Numbers indicate bootstrap values based on 100 pseudo-replications. The mitochondrial tRNA sequence data set was subjected to MP (bootstrap values upper of each triplet of numbers), NJ (bootstrap values in the middle of each triplet of numbers), and ML (bootstrap values lower of each triplet of numbers) analyses. 

Figure 9.9 50 per cent majority-rule consensus bootstrap trees based on the mitochondrial protien data on the set using lamprey and hagfish as outgroup. 

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).

Fig. 7.4 The tree is based on full-length sequences, and constructed by using the neighbor-joining method. Bootstrap values (% from 1,000 replications) are indicated. NodA sequences of published rhizobia are available in GenBank. A, Azorhizobium, B, Bradyrhizobium. M, Mesorhizobium. Me, Methylobacterium. R, Rhizobium. S, Sinorhizobium (Moullin et al. 2001)...

The main alternatives to bootstraps are usually method specific (see Li and Gouy, 1990 for a review). For example, one can calculate how many steps in a parsimony analysis two trees must be apart for one to... 

Fig. 10. The tree from Fig. 1 with bootstraps shown for the four internal branches. This is a neighbor joining tree, which is originally unrooted. It is shown with a root here for cosmetic purposes, but there is no bootstrap information for the two groups split by this root.

Fig. 4. The evolution of the globular domain of histone HI. (a) The parsimony tree for the structure of the wing subdomain of GHl. The length of the insert was calculated from the alignment of the GHl sequences, (b) The parsimony tree for histone HI based on sequences of GHl domains of known HI histones. Percentage values on each branch represent the corresponding bootstrap probabilities. Branches for which the relationships are unclear (supported by less than 50% probability) are marked by thin lines. Reproduced with permission from Ref. [72],...

Fig. 11.4 Sequence comparison of Arabidopsis geranyllinalool synthase with other Arabidopsis TPS and putative or characterized linalool and geranyllinalool synthases from Clarkia, Medicago, poplar and grape. A neighbor-joining tree generated from an amino acid sequence alignment (QustalX) of 13 TPS proteins is shown. Numbers are bootstrap values higher than 800 out of 1,000 replicates. TPS proteins belong to different families as indicated by letters. V. vinifera putative GES, Acc. 002268557 P. trichocarpa putative GES, Acc. 002305640...

Fig. 1. Unrooted phylogenetic tree based on the core amino acid sequences of 113 catalases. The numbers at the three main nodes represent the proportion (out of 100) of bootstrap sampling that supports the topology. The three main clades are circled for clarity.

Twenty-two clusters could be unambiguously detected from the present analysis of 30 amino acid positions (Fig. 5). These clusters were defined in order to encompass the maximum number of related entries within a branch characterized by the highest possible statistical bootstrap value. Thirty-four out of 372 entries could not be assigned to one of the existing 22 clusters and are considered as singletons. The herein presented tree... 

You run the unknown compound through each of the trees in the forest and average the predictions that the different trees make for it. The term bagging is a contraction of bootstrap aggregating, and so it would seem to apply only to forests created by bootstrapping, but in fact bagging is effective also with RRP forests. 

A) A distance matrix was constructed from the inferred amino acid sequences using a Poisson correction for multiple hits and the tree constructed using the minimum evolution approach. Five hundred bootstrap resamplings were carried out. Branches with bootstrap support values less than 50% are indicated with an asterisk. 

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).

Figure 14.3 A neighbor-joining tree of most OBPs listed in Table 14.2 bootstrap support is based on 1000 replicates and only branches with >50% support are shown. A single tree is shown, broken into thirds to fit the page. Insert A is a key to the taxa. Insert B is the uncollapsed tree (taxa not shown) to illustrate full branch lengths (percent sequence differences). A size bar indicating 10% sequence difference is shown. Named clusters (e.g. ABPX) are referred to in the text.

Figure 18.1 Neighbor-joining tree selected members of the PBP protein class, based on 1000 bootstrap replicates (Clustal X 1.8 Saitou and Nei, 1987 Thompson et al., 1997). Relative branch lengths are indicated by the scale bar. Two groups of PBPs within Noctuidae are clearly revealed. Group 1 (Grp 1) Aips-1/Aseg-1/Mbra-2/Hvir-1/Hzea-1 Group 2 (Grp2) Aips-2/Aseg-2/ Mbra-1/Hvir-2.

Figure 18.4 A Phylogenetic relationships of moth ABPXs and DmeIPBPRPs. The primary sequences of the proteins were aligned in Clustal X 1.8 and processed using PAUP 4.0d65 (Swofford, 1999). The tree represents equally most parsimonious trees of 909 steps and consistency index 0.52. The numbers above each branch indicate the percent bootstrap support above 50 percent for the supported node using maximum parsimony (Felsenstein,...

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