BAMBE

Bayesian Analysis in Molecular Biology and Evolution

Version 2.03 beta, January 2001

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

Glossary

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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