Neighbor-Joining tree

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.

GPCR phylogenetic analysis partial neighbor-joining tree of the rhodopsin receptorlike family (A) from Joost andMethner (Genome Biol., 3 research 0063.1-0063.16,2002. http //genomebiology.com/ 2002/3/11/ research/0063). Detailed receptor names are provided in the additional data file 1 of the reference. 

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...

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 5.2 Neighbor-joining tree of sequence similarity in the 7TM domains of human monoamine-related GPCRs. The receptors are coded according to the SwissProt nomenclature scheme orphan receptors are coded with the prefix GPR followed by an index number. Distance corresponds to percent sequence identity, scale is indicated by a 5% bar. The tree is rooted by outgrouping the node of the H, and muscarinic receptors. The numbers on the branches are the result of bootstrap analysis (1 OCX) replicates). For further details see [60].

Figure 5.7 Neighbor-joining trees of the sequence homology of each binding site for monoamine-related GPCRs. The underlying sequence blocks correspond to transmembrane residues identified within the 6-A contact spheres of 5-HT (panel A), propranolol (panel B) and 8-OH-DPAT (panel C), respectively, in the rho-dopsin-based models of the 5-HT1A receptor-ligand complexes. Details as in the legend for Figure 5.2.

Figure 10. Neighbor-joining trees of lysin and 18K proteins from the five species. The scale bar shows amino acid p-distances. The topology of both trees is the same, however 18K is two to three times more divergent than lysin (from Vacquier et al., 1997).

Figure 6 Neighbor-joining tree showing the phylogenetic relationship of Desulfomicrobium sp. str. Ben-RB with species of the genus Desulfomicrobium and other members of the 5-Proteobacteria. The sequence of Escherichia coii was used as the outgroup. Significant bootstrap values from 100 analyses are shown at the branch points of the tree. Bar = 0.01% sequence difference. (From Ref. 9.)...

Based on the initial results above and the desire to create a universal bacterial assay, we decided to limit further analysis to fragment masses derived from only the Lane-AB or Lane-BC amplicons. Figure 43 contains a neighbor-joining tree of all explicitly named... 

FIGURE 4.3 Neighbor-joining tree of all explicitly named NIAID Category A, B, or C bacterial pathogens as resolved by base-specific fragmentation of the Lane-AB amplicon and spectral distances derived from the presented coincidence function Separation of some of the unresolved clusters may be improved by further mass spectrometric analysis of the Lane-BC sequence region. 

B—neighbor-joining tree (Jukes-Cantor distance matrix and 500x bootstrap) ... 

On the other side, maximum likelihood tree (out of 211 tested) placed Australian C. phalaridis basal to the group 2, whereas American C. paspali and C. citrina were closer to the ancestors of group 1. The branches with zero length were collapsed to polytomies. The neighbor-joining tree resembles the ML tree (with the exception of C. phalaridis) and their log likelihoods were almost identical (ML=-990.245 NJ =-990.256). The NJ tree branches supported by less than 50% bootstraps were reduced to polytomies. 

Fig. 2. PIRSF protein family report. Includes (A) DAG browser displaying the PIRSF family hierarchy (B) taxonomy tree browser displaying the taxonomy distribntion of all family members (C) tree viewer with neighbor-joining tree and (D) alignment viewer displaying ClnstalW mnltiple alignment of seed members. This report can be viewed directly at http //pir.georgetown.edu/ cgi-bin/ipcSF id=PIRSF000514.

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