Neighbour-joining analysis

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

Fig. 11.2. Neighbour-joining phylogenetic tree of the predicted peroxiredoxins shown in Fig. 11.1. This unrooted tree was generated using the computer program PHYLIP (Felsenstein, 1989) version 3.5c. GenBank accession s of the sequences used in this analysis are shown in Fig. 11.1 legend.

Neighbour-joining (NJ) analysis with approximate correction for among-sites rate variation was applied to an alignment, which did not incorporate weakly homologous sequences. Species or even phyla characterized by long branches were additionally excluded. 

Figure 1. The phylogenetic relationship among the trypanosomatid deacetylases and other class l/li deacetylases. Related proteins were identified by BLAST analysis. The unrooted neighbour-joining tree was generated using Clustal 1.8X and TreeView. The two classes and the trypanosomatid enzymes (DAC1 -4) are highlighted and all accession numbers are shown. Tb, T. brucei) Tc, T. cruzi Lm, L major, Hs, Homo sapiens Sc, S. cerevisiae Cl, Ciardia lamblia Eh, Entamoeba hiostolytica Pf, Plasmodium falciparum.

Fig. 12. Schematic procedure for cluster analysis. Original data points are shown as letters a-j the sequence of joining nearest neighbours and replacing them with the centroid is shown numerically. The dendo-gram is shown below, the lengths of each branch being approximately proportional to the distance between the points or locates being joined...

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