© Copyright 2000, 2001, Donald Simon & Bret Larget, Department of Mathematics and Computer Science, Duquesne University.

**Clade**- For an unrooted tree, a clade is a group of taxa that may be separated from the rest of the tree by breaking a single branch. For a rooted tree, a clade is all taxa in a subtree of the tree.
**GNU**- "GNU's not UNIX".
Free software (such as the C compiler
`gcc`

, the C++ compiler`g++`

, and the graphing program`gnuplot`

) are available at the ftp site`prep.ai.mit.edu`

. **Internal node**- A non-leaf node of the tree. An internal node has more than one edge.
**Labeled history**- A description of the tree that includes the tree topology and the relative times of all the branching points of the tree, but does not include branch length information. A single tree topology may have many labeled histories.
**Markov chain**- A sequence of random variables in which the distribution of each random variable depends only on the value of its predecessor.
**Markov chain Monte Carlo**- A computational technique for the numerical evaluation of high-dimensional integrals by simulating a Markov chain on a parameter space.
**Metropolis-Hastings**- The main form of Markov chain Monte Carlo. The algorithm provides a probabilistic rejection rule to reject some proposed moves of an arbitrary irreducible Markov chain so that the resultant Markov chain has the desired stationary distribution.
**Newick format**- A parenthetic representation of a tree with a colon and branch length following every proper subtree of the tree. A more complete description of the format and the history of its name is described in the documentation of Joe Felsenstein's PHYLIP suite of programs.
**Phylogeny**- A tree that describes the evolutionary history of a group of species or taxa.
**Prior distribution**- The probability distribution of one or more parameters before observation of data.
Ideally, it represents the prior belief of the researcher.
Frequently, a flat, ignorance prior may be adopted.
**Posterior distribution**- The conditional probability distribution of one or more parameters,
after observation of data.
The posterior distribution is proportional to the product of the likelihood
and the prior distribution.
A
**joint posterior distribution**describes the distribution of more than one random variable. **Tree topology**- The shape and leaf labeling of the tree. The tree topology disregards branch lengths and the relative times at which speciation events that do not involve ancestors occur. A single tree topology may represent more than one labeled history.

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This page was most recently updated on January 19, 2001.

bambe@mathcs.duq.edu