About SIMMAP Software
SIMMAP is a post tree analysis program for making inferences about molecular and morphological character evolution. SIMMAP is similar in purpose to MacClade. Inferences are based on sampling character histories from the posterior distribution of character histories on a phylogeny. SIMMAP does not rely on parsimony, but employs a new method for the stochastic mapping of characters (see Nielsen, 2002). SIMMAP was written for scientists interested in the analysis of character evolution and educators teaching about the principals of stochastic models of sequence evolution.
- Stochastically map molecular or morphological characters (mutations) on a phylogeny.
- Estimate covariation between molecular or morphological characters.
- Estimate dN and dS, while accounting for model and tree uncertainty.
- Estimate a wide variety of descriptive statistics for patterns in molecular or morphological evolution.
- Use sampling from predictive distributions to approximate null distributions and assign significance (covariation, dN, dS).
- Manipulate data sets and trees.
- Many more... (see help documents for more information)
SIMMAP was written for Apple's Mac OS X operating system. It is compatible with OS versions 10.3.9+ (However, recent fixes and new features have not been tested on versions before 10.4). Unfortunately, SIMMAP will not run on OS 10.2 or earlier. For more information on SIMMAP development and system requirements, click here.
Some Published Papers Using SIMMAP
McLeish, M. J., Chapman, T. W., and M. P. Schwarz. (2007) Host-driven diversification of gall-inducing Acacia thrips and the aridification of Australia. BMC Biology. 5:3.
Leschen R. A. B. and Buckley T. R. (2007) Multistate characters and diet shifts: Evolution of Erotylidae (Coleoptera). Systematic Biology 56(1): 97-112.
Pereira S.L., Johnson K.P., Clayton D.H., et al. (2007) Mitochondrial and nuclear DNA sequences support a cretaceous origin of columbiformes and a dispersal-driven radiation in the paleogene. Systematic Biology. 56(4): 656-672.
Wanke S., Vanderschaeve L., Mathieu G., et al. (2007) From forgotten taxon to a missing link? The position of the Genus verhuellia (Piperaceae) revealed by molecules. Annals of Botany. 99(6): 1231-1238.
Raffiudin R. and Crozier R. H. (2007) Phylogenetic analysis of honey bee behavioral evolution. Molecular Phylogenetics and Evolution. 43(2): 543-552.
Turner L. M. and Hoekstra H. E. (2006) Adaptive evolution of fertilization proteins within a genus: Variation in ZP2 and ZP3 in deer mice (Peromyscus). Molecular Bioloogy and Evolution. 23(9): 1656-1669.
Bulmer, M.S. and R.H. Crozier. (2006) Variation in positive selection in termite GNBPs and relish. Molecular Biology and Evolution. 23(2):317-326.
Jones, W.J., Won, Y-J., Maas, P.A.Y., Smith, P.J., Lutz, R.A. and R.C. Vrijenhoek. (2006) Evolution of habitat use by deep-sea mussels. Marine Biology. 148(4):841-851.
Baker, A.J., Pereira, S.L., Haddrath, O.P., and Edge, K-A. (2006) Multiple gene evidence for expansion of extant penguins out of Antarctica due to global cooling. Proceedings of the Royal Society B: Biological Sciences. 273(1582):11-17.
Lewis, L and P. Lewis. (2005) Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta). Systematic Biology. 54(6):936-947.
Aanen, D.K. and P. Eggleton. (2005) Fungus-growing termites originated in African rain forest. Current Biology. 15(9):851-855.
Chaverri, P., Bischoff, J.F., Evans, H.C., Hodge, K.T. (2005) Regiocrella, a new entomopathogenic genus with a pycnidial anamorph and its phylogenetic placement in the Clavicipitaceae. Mycologia. 97:1225-1237.