Overview

The name SIMMAP is an acronym for StochastIc Mutational MApping on Phylogenies. SIMMAP is a post-tree analysis program for exploring and analyzing a character's mutational history. The characters of interest might be DNA/RNA sequences or standard (morphological) characters. Unlike other commonly used programs (e.g., MacClade) for mapping characters, SIMMAP does not rely on parsimony. It implements a Bayesian method called "Bayesian Mutational Mapping (BMM)" (Neilsen, 2002) for mapping characters using stochastic substitution models. SIMMAP summarizes character maps (number of changes, kinds of changes, etc.) and uses sampling from posterior predictive distributions for evaluating statistical significance, of a number of hypotheses, through the use of predictive p-values.

Feature List

1. Stochastically map molecular (nucleotide and codon states) or morphological characters on a tree.
2. Estimate covariation between molecular (nucleotide only) or morphological characters to test hypothese of correlated evolution.
3. Estimate dN and dS, while accounting for model and tree uncertainty. Using sampling from predictive distributions users can test for positive selection at a site(s).
4. Estimate a wide variety of descriptive statistics for patterns in molecular or morphological evolution. For example, tranisitions, transversions, amino acid usage and direction of changes, bias in two state morphological states, and among many others, covariation statistics.
5. Use sampling from predictive distributions to approximate null distributions and assign significance (covariation, dN, dS).
6. Manipulate data sets and trees. Users can modify both the data matrix and the trees to alter the contents of an analysis. In addition, users can modeify a data matrix and save it to a new file and even save the data as amino acid residues choosing from 12 different genetic codes.
7. Trees with or without a character mapped onto them can be copied and then pasted into a graphics application for publication quality files or talks and seminars.
8. Too many other features to list here...

System Requirements

SIMMAP was written for Apple's Mac OS X operating system. It is compatible with OS versions 10.3+ and is also available as a Universal Binary for use on Intel Macs. [The SIMMAP Universal Binary has not been tested on an Intel Mac but has been tested on a G4 Mac without any difficulties.] It may also operate normally on version 10.2 but no gaurantees are made.

Future Developments and Platforms

For a preview of the upcoming version see the SIMMAP 2 website here.