|Welcome to the SIMMAP web site!
The final update, SIMMAP 1.5, is finished and in the final testing phase. Version 1.0 will no longer be supported but will still be made available until some future date. Please migrate your usage to the new version here.
SIMMAP is a post tree analysis software package for stochastically mapping characters (mutations) on phylogenies. It uses an "indirect" approach as first developed by Nielsen (2002). The name SIMMAP is an acronym for StochastIc Mutational MApping on Phylogenies.
SIMMAP has been developed to implement stochastic character mapping that is useful to molecular
evolutionists, systematists, and bioinformaticians. Stochastic mutational mapping, as implemented in the SIMMAP software, enables users to address
questions that require mapping characters onto phylogenies using a probabilistic approach that does not rely
on parsimony. Analyses can be performed using a fully Bayesian approach that is not reliant on considering a
single topology, set of substitution model parameters, or reconstruction of ancestral states. Uncertainty in these
quantities are accommodated by using Markov chain Monte Carlo (MCMC) samples from their respective posterior distributions. Researchers can address questions about positive selection,
patterns of amino acid substitution, character association, and patterns of morphological evolution.
SIMMAP.com now uses Google's site search to perform searches of the website pages. To search the website simply select Search from the pulldown menu at the top right of the page or select the button at the bottom of each page. The web site has been designed to enhance the user experience making it easier to access information about the SIMMAP software. The web site can be navigated using the pull down menu at the top right of the site. The Help Pages are being brought up to date and current with the SIMMAP distribution. If you are currently using SIMMAP or trying it out and the help documents for a topic you are interested isn't yet up to date, email and I will try to help out . If you want to contribute to a topic or a tutorial send me an email with the text (html or plain text) and I will review it and make it available on the web site.
Current Distribution: Version 1.0 Beta 2.4 (Build 03032009-1.0-B2.4)
See the News page from more information on this update.
Bugs: Update strongly recommended!
- Fixed a problem in which the size of some the program windows clipped or masked their contents.
- Fixed an issue that would cause the program to crash -- all analyses -- when running on Intel Macs. This bug has been fixed. Since the bug resulted in a program crash and was related to management of the memory pool there is no reason to believe it effects any results.
- Fixed a number of interface issues associated with the previous version of SIMMAP running on machines operating the new version of the Mac OS (10.5). The primary issue pertained to the built in help documents. These are still available but will be displayed by the user's default web browser. All of the issues were associated with the GUI interface and therefore did not effect analyses.
- Fixed an underflow issue associated with running large molecular analyses. The results from such analyses report NAs rather than actual values.
- Fixed the bug that caused a program crash after pruning taxa from the trees. The pruning taxa option now permanently removes both the taxa from trees and from the data matrix in memory. The original files are not effected.
- Fixed the bug that would cause a crash after all of the files (molecular data) are closed and new files (particularly the parameter file) are opened.
- Fixed minor spelling mistakes in the interface and some object focus issues.
See the bugs page for more information.
Download Application Note: Please cite this when publishing or presenting results derived from using SIMMAP. A copy of this pdf is also distributed with the download.
Bollback, J. P. (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics. 7:88.