Glossary of terms used in Phylogeny Reconstruction.
Decay Analysis Also known as Bremmer Support is a method of analysis that seeks to find theshortest tree that is incompatible with a pre-specified clade. In other words, we look for the shortest tree that does not contain the clade of interest. The number of steps that are taken in order to break this internal branch is the Decay Index or Support Index for this clade.
Decay Index see Decay Analysis. A number that corresponds to the number of steps required to break the clade defined by a certain internal branch.
Distance Matrix (DM) This is a pairwise 'distance' between taxa, based on some observation. For molecular data, it could be the observed number of nucleotide differences between the pairs of taxa, alternatively, it could be the reconstructed distances between these sequences (based on some model of sequence evolution). It could equally be based on morphological data (although this is out of favour as a method), immunological data, ecological data or behavioural data. It is possible to use a distance matrix in order to construct a dendrogram indicating the similarities between pairs of taxa. See UPGMA or Neighbor-joining.
Duplication This is a genetic event that results in a region of DNA being copied to another part of the genome. The result is that the genome now has a new paralog of the original gene.
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