Glossary of terms used in Phylogeny Reconstruction.




Nearest Neighbor Interchange (NNI) This is a heuristic algorithm for searching through treespace.  It proceeds by juxtaposing the positions of neighbors on a phylogenetic tree.  If the resulting tree is better, then it is retained.  This algorithm is quite a gentle perturbation of the tree and is inferior to either SPR or TBR in terms of completeness of the searsh.  On average it will be quicker than SPR or TBR.

Nexus-format This is a format that has been published in:   Maddison, D.R., D.L. Swofford, and W.P. Maddison. Nexus: An extensible file format for systematic information. Systematic Biology 46(4) 1997: 590-621.

Neighbor-Joining (NJ) This is an algorithm for inferring a branching tree diagram from a distance matrix. It works by successively clustering pairs of taxa together.  It is related to the UPGMA method of inferring a branching diagram from a distance matrix.  Unlike the UPGMA method, NJ can facilitate contemporary tips of uneven length.  This makes it a more appropriate tree reconstruction method than UPGMA in thos instances when evolution has not proceeded in a strictly clock-like fashion.

Newick format This is a method of representing trees using nested parentheses. Two sister taxa are enclosed in a pair of parentheses, separated by a comma.  If the closest relative of these two taxa is another single taxon, then all three taxa will be enclosed within another pair of parentheses.  In this way, a complete tree description may be built.  This format is also called the New Hampshirt format.  Apparently it is named after a restaurant in New Hampshire, USA.

NNI see Nearest Neighbor Interchange.

Non-synonymous substitutions Substitutions that occur in protein-coding genes that result in a change at the amino acid level.  The ratio of non-synonymous to synonymous substitutions is sometimes used to detect positive Darwinian selection.


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Any Questions? email: James Mcinerney