Xml Input File
Data View
Include/Exclude Chars
Genetic Codes
Saving Data
Export Data
Tree View
Assign Branch Lengths
Rooting Trees
Print Trees
Export Trees
Output Files
Substitution Models
Morphology Priors
Analysis (Mapping)
Mapping Statistics
Analysis (Correlation)
Correlation Statistics
Analysis (Selection)
Selection Statistics
Analysis (ASR)


To explore different aspects of the program select an option from the menu at the left. Since SIMMAP 1.5 is a fairly radical update to version 1.0 you may wish to first take a look at the Xml file format -- this will be particularly useful if you are already familiar with version 1 as 1.5's other features are very similar in most respects.

What is stochastic mutational mapping?

A stochastic mutational map is a description of the historical pattern of states along a phylogeny or genealogy. The method was first described by Nielsen in 2001 and 2002, and was then extended to standard characters in 2003 by Huelsenbeck and others. There are three primary components of a mutational map (see figure below). The first component is the ancestral state reconstruction at each node in the phylogeny. Second, the occurence and timing of different states on the tree. Lastly, the location (timing) of changes along the phylogeny.

A mutational map is more than just a simple description of the ancestral reconstructions at the internal nodes of the tree. As an aside, SIMMAP 1.5 does allow the calculation of ancestral states, however these are not derived from the mutational map but rather are calculated directly as the marginal posterior probability of each possible character state.

How is stochastic mutational mapping different than parsimony mapping?

For more information (I recommend reading these to fully understand the methods in SIMMAP):

Nielsen R. Mutations as missing data: inferences on the ages and distributions of nonsynonymous and synonymous muta- tions. Genetics 2001, 159:401-411.

Nielsen R. Mapping mutations on phylogenies. Syst Biol 2002, 51:729-732.

Huelsenbeck JP, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Syst Biol 2003, 52:131-158.

Bollback JP. Posterior mapping and predictive distributions. In "Statistical methods in Molecular Evolution" (Nielsen, R. Ed.) Springer Verlag New York, Inc. New York, USA. 2005.

Bollback JP. SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 2006, 7:88.

Bollback JP., PP. Gardner, and R. Nielsen. Estimating the history of mutations on a phylogeny. In "Ancestral Sequence Reconstruction" (Liberles, D. Ed.) Oxford University Press, UK. 31 May 2007.

Is stochastic mutational mapping the same as ancestral state reconstruction (ASR)?

The short answer is no. Ancestral state reconstruction is a method that reconstructs ancestral states at the internal nodes of the tree. In the case of probablistic approaches this produces probabilities for each possible state at each node. The reconstructions can be either marginal or joint (however, the ASR option in SIMMAP 1.5 gives the marginal probability). The ASR option in SIMMAP 1.5 does not use stochastic mutational mapping (which employs a joint distribution sampler) to determine the ASR probabilities. An ASR analysis does not explicitly provide information about the timing and placement of different changes or the duration of different states - stochastic mutational mapping does (see figure above).