Like other apicomplexan parasites forming environmentally resistant oocysts, e.g., Eimeria spp. and Cryptosporidium spp., T. gondii stores glucose in cytoplasmic granules of amylopectin, a polysaccharide consisting of long linear chains of glucose units linked by α-1,4-glycosidic bonds, with occasiona1α-1,6-glycosidic bonds providing a branching point [ 37].
Sankoff originally provided a branch-and-bound algorithm.
Next, a reference tree was needed providing a topology and branch lengths and including all of the species studied.
Using the GeneMaths option Cluster Plot (see Methods section for details) provided a recommended branch cutoff level of 88% cluster similarity.
Degnan and Rosenberg (2006) provided a critical branch length below which gene trees are susceptible to the AGT problem.
This is an attractive route to the target system via the bis-halogenated quinoline 12, which provides a suitable branch point for the rapid preparation of analogues.
Branch models were used to test for significant differences in dN/dS between the bottlenose dolphin and the cow (divergence c. 50 my), between the elephant and the hyrax (divergence c. 80 mya), and between humans and the bushbaby (chosen to provide a similar branch length, divergence c. 80 mya).
After culling to eliminate partitions with too few taxa to provide phylogenetic resolution, remaining neutral scores belong to partitions that presumably have no impact on the phylogeny and have a minimal evolutionary signature for each branch; thus, providing a null hypothesis of GO term overrepresentation and contribution to a particular branch.
In insects requiring increased sensitivity, the antennae are branched, providing a larger surface area on which more sensilla can be accommodated.
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