Clade- This is a monophyletic group.

Cladistics- (1) The Journal of the Willi Hennig Society. (2) The scientific discipline of classifying organisms according to the doctrine of Willi Hennig's 1966 book. (3) The belief that the organisation of taxa into groups can only be done by the identification of synapomorphies for that group.

Cladogram- A dendrogram depicting the hypothesised branching order of a number of sequences. Cladograms do not give any indication of temporal change, unlike a phylogram which does.

Clock- also known as a molecular clock.  One of the most important assumptions that is often made using molecular data is the existence of a clock.  In other words, there is sometimes an assumption being made either implicitly or explicitly that the rate of change of residues in molecules is approximately constant.  Making this assumption is fraught with dangers, but a great many empirical studies have shown that (with some errors) the assumption of a clock often holds true.  If there are some good reference points (say, fossils or significant geological events) it is sometimes possible to use molecular data to estimate the time of events for which there is no other alternative.

Clustal- The name of a program for performing automated multiple sequence alignment.  The original program was written by Desmond G. Higgins when he worked as a post-doc in Paul Sharpe's lab in Dublin, Ireland.  In its present incarnation, Clustal is available as a text-only program called ClustalW or as a graphical program, with pull-down menus, called ClustalX.

Codon- This is a group of three adjacent nucleotides that encode an amino acid.  The identity of the encoded amino acid can vary for a particular codon, depending on the genetic code that is in use by an organism.

Congruence- Agreement between characters or trees.

Consistency Index (CI)- This is a measure of how well an individual character fits on a phylogenetic tree.  It is calculated by dividing the minimum possible number of steps by the observed number of steps.  If the minimum number of steps is the same as the observed number of steps, then the character will have a CI of 1.0.  If a character is not completely compatible with a tree, then it will have a CI value less than 1.0.  The CI value of a tree is the average CI value over all of the characters.  There are two problems with this value.  It is expected to decrease with increasing numbers of taxa and it is not clear what value is acceptably high or low.

Constraint- This term usually refers to the placement of a caveat on the search algorithm, so that it never examines trees that are pre-specified by the user as being unwanted or unlikely.  Constraint analysis is often used to speed-up the search through tree-space.  If a search is constrained so that it does not look at improbable relationships (and therefore does not evaluate these topologies), then it might proceed much more quickly.  On the other hand, constraint analysis might proceed by only finding those trees that are incompatible with the constraint tree (reverse constraint analysis).  The latter analysis is used in order to place Decay Indices on the internal branches of a tree.

Convergence- An evolutionary event which occurs in two independent sequences. If the sequences possess two different character states for a particular character, but change results in each of these characters independently acquiring an identical character state, this is said to be a convervence. Convergences differ from parallellisms because the ancestral sequences are not the same. In parallellisms, the ancestral sequences are the same.

Choose the first letter of your term.

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Any Questions? email: James Mcinerney