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