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SIMMAP20

SIMMAP20

Owned by Sheldon McKay
Last updated: Aug 24, 2009Version comment

Prepared by: Zhenyuan Lu

Tool Name: SimMap 2.0

Homepage: http://www.simmap.com/v2.0/index.html

Platforms: Mac OS X, Linux, Windows

Implementation Language: C++

Documentation/Manual: http://www.simmap.com/v2.0/pgs/docs.html

Purpose of Program:
SIMMAP 2 is a post tree analysis software package for stochastically mapping mutations on phylogenies.

Description of Program:
Jonathan Bollback, of the Bioinformatics Centre of the Institute of Molecular Biology and Physiology (IMBP) at the University of Copenhagen, Denmark (bollback (at) binf.ku.dk) has written SIMMAP (SIMulation MAPping).

SIMMAP 2 implements stochastic mutational mapping using a wide range of models: 4 x 4 general reversible nucleotide models - Jukes and Cantor to GTR; doublet RNA models; codon models; amino acid models; and, standard Mk character models. The stochastic mutational maps generated by SIMMAP 2 can be used to address a variety of evolutionary questions. Included in the standard distribution are analysis modules for addressing questions about patterns of character evolution (e.g., biases in substitutions), correlated character evolution, reconstruction of ancestral states, and testing evolutionary rates (e.g., dn vs. ds). In addition, the SIMMAP 2 software package includes a basic Phylo module that aids in the development of custom analyses.

SIMMAP 2 was written to replace the graphical user interface (GUI) version written for Mac OS X, SimMap 1.0 (Bollback, 2006). This new incarnation is being co-authored by Jiaye Yu.

With this re-write we wished to accomplish a number of goals:

1. To provide a program that is available across all the major operating systems (e.g., Windows, Macintosh OS X, Unix, and Linux). SIMMAP 2 will be compatible with any OS that has a C++ compiler that supports the C++ STL library. The software will be distributed as source code (see License) or as executable binaries. Use of the analysis modules will require the installation of Python.
2. To expand the capabilities of the program to include support for polytomies in the phylogeny, expand the number of models (all general 4X4 nucleotide models, doublet RNA models, codon models, amino acid models), increase the number of states in the Mk models (around 30), and support analysis with heterogeneous models using character (site) partitions.
3. To modularize statistical analysis of mutational histories allowing for easy and flexible user customization.
4. To provide support for multiple processors and add parallel processing capabilities.

SIMMAP 2 download is not available yet.

Inputs:
No documentation yet. It is likely the same as SimMap 1.0

Outputs:
No documentation yet. It is likely the same as SimMap 1.0

Relevant publications:

  • Nielsen, R. 2002. Mapping mutations on phylogenies. Systematic Biology 51: 729-739.
  • Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology 52: 131-158.
  • Bollback, J. P. 2006. SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7:88.

Related Tools:

  • SimMap 1.0
  • MacClade