RID - Visualization tool

Version 1.0

 ©Kent Vander Velden and Gavin Naylor

Iowa State University


Dirac Science Library,
Florida State University,
Tallahassee, FL 32306-4120



RID - This software allows users to detect phylogenetic misleading sites in a within multiple alignments.


Different genes often yield different phylogenetic trees for the same set of taxa. This is often ascribed to stochastic variation in the evolutionary process. However there are many circumstances in which stochastic variation is inadequate to explain the strikingly different well-supported topologies that result from the analysis of different genes. In such circumstances it is likely that there are signals in one or other (or both) genes that are misleading. Biologists would like to identify the residues responsible for such phylogenetically misleading signals to both improve phylogenetic estimation and to explore the underlying forces responsible for the signal conflict.


We have developed a method to identify residues that show the maximum difference in phylogenetic fit between two alternative hypotheses. The method is based on the idea that if a residue fits one topology well and another badly it must be phylogenetically influential (positively or negatively) with respect to the alternative hypotheses being considered . If the residue fits a credible tree poorly and an unlikely tree well, it is likely that  the residue is phylogenetically misleading and vice-versa.
If stochastic variation in the evolutionary process is responsible for different genes yielding different phylogenetic inferences, we might expect the distribution of misleading residues to be scattered randomly over the structure of the molecule. If, on the other hand, a molecular mechanism is responsible for  a misleading signal it is more likely that  misleading residues will appear localized and clustered in one part of the molecule.


Movies showing two study cases are available: (1) Hemoglobin alpha chain (2) Cytochrome b
In the movie at left we show  the tree depicting the widely accepted phylogenetic tree. At the right is the phylogenetic tree yielded by a parsimony analysis. In the center is a structural modelof the crystal structure of the studied protein showing the most phylogenetically misleading residues in color.(Phylogenetically misleading residues are those with a good fit to the tree yielded by the parsimony analysis and a poor fit to the true tree). The fit of each character was measured with the retention index.

You will probably need one of the following media plug ins (freeware):

Real Player Quick Time Media Player


Click to enlarge
Identify misleading sites
Swiss prot parser


A Unix version and Windows version of the software are available.

Naylor Laboratory
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