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Glossary

Character

A character is some feature, either physical or genetic, that divides a collection of taxa into two groups. The ultimate goal is to apply characters to the construction of a phylogeny, where taxa are represented as the leaves of a tree.

There are two common ways of encoding a given character C dividing a collection of n taxa. C can be written in split notation as SSc, where S is a subset of our taxa and Sc is the set complement of S. Removing an edge from a tree divides its leaves into two disjoint sets S and Sc, so that we can establish a correspondence between characters and edges of the phylogeny: specifically, we may assign each character to the edge that its split notation implies.

The second notation for C assumes that we have ordered our n taxa, after which C may be written in array notation as an array A in which A[i] is equal to 1 or 0 depending on whether the ith taxon belongs to S or Sc. Given a collection of arrays from a number of different characters, we may combine the arrays into a matrix called a character table. The creation of a phylogeny from a character table is an important algorithmic problem.

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