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SIMMAP10

SIMMAP10

Prepared by: Zhenyuan Lu

Tool Name: SimMap 1.0

Homepage: http://www.simmap.com/v1.0/simmap.html

Platforms: Mac OS X

Documentation/Manual: http://www.simmap.com/v1.0/pgs/help.html

Purpose of Program:
SIMMAP is a post tree analysis program for making inferences about molecular and morphological character evolution.

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) version 1.0 Beta 2.4. 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.

  • 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.

SIMMAP is a Mac OS X executable, available from its web page at http://www.simmap.com/simmap/simmap.html at the University of Copenhagen. (Source: Phylogeny Programs)

Inputs:
The full heirarchical Bayesian treatment requires three or two files for analysis of molecular and morphological data, respectively. SIMMAP can be used with only a data file and tree file (or a data file containing a tree block after the data block) to explore character evolution. The data file should contain a DNA or morphological data matrix, the tree(s) file should contain a trees block containing trees in the Newick format.

Data file:
The data file should conform to the basics of the Nexus format standard. Currently, the data matrix can not be interleaved. However, the file can contain spaces intersperced within the sequence. In addition, the symbols '?', '-', and N's are treated as uncertain and all possibble states have equal probability while calculating conditional likelihoods. The '.' character can be used as an abbreviation for the last state fully defined in the column.

Tree file:
The tree file is a text file in standard Nexus format with a translate command followed by a listing of trees. axon names in the Newick tree representation are NOT permitted and the translate command must use integers to identify taxa in the trees.

Outputs:
Individual Statistics File:

Statistics collected during an analysis of posterior histories. The following are the tab-delimited column's contents (not in the order they appear in the file):
Header Description
Rep Replicate number
Tree Tree number (numbering defined by input file order)
Nstates Number of character states (morphology only)
Site Site number (numbering defined by input file order)
Bias Bias parameter (morphology only)
Rate Gamma rate parameter (morphology only)
HI Homoplasy index, NOT IMPLEMENTED (morphology only)
Trans The number of changes (morphology only)
Subs The number of substitutions (molecular only)
Ti The number of transitions (molecular only)
Tv The number of transversions (molecular only)
Syn The number of synonymous changes (molecular (codon) only)
Nsyn The number of non-synonymous changes (molecular (codon) only)
Radical The number of radical amino acid changes (molecular (codon) only)
Conserv The number of conservative amino acid changes (molecular (codon) only)
DeltaHydrop The average change in hydropathy along the phylogeny (molecular only)
AvgHydrop The average hydropathy along the phylogeny (molecular only)
i=>j Number of changes from state i to state j
t(i) Dwell time in state i

Summary Statistics File:

Header Description
Rep Replicate number
Tree Tree number (numbering defined by input file order)
Nstates Number of character states (morphology only)
Site Site number (numbering defined by input file order)
Bias Posterior expectation of bias parameter (morphology only)
Rate Posterior expectation of gamma rate parameter (morphology only)
HI Homoplasy index, NOT IMPLEMENTED (morphology only)
Trans Posterior expectation of the number of changes (morphology only)
Subs Posterior expectation of the number of substitutions (molecular only)
Ti Posterior expectation of the number of transitions (molecular only)
Tv Posterior expectation of the number of transversions (molecular only)
Syn Posterior expectations of synonymous changes (molecular (codon) only)
Nsyn Posterior expectations of non-synonymous changes (molecular (codon) only)
Radical Posterior expectation of radical amino acid changes (molecular (codon) only)
Conserv Posterior expectation of conservative amino acid changes (molecular (codon) only)
DeltaHydrop Posterior expectation of average change in hydropathy (molecular only)
AvgHydrop Posterior expectation of average hydropathy (molecular only)
i=>j Posterior expectation of number of changes from state i to state j
t(i) Posterior expectation of the dwell time in state i

dN/dS Raw Statistics File:

SIMMAP allows dN and dS values along a branch to be saved to a file allowing the user to test for positive selection on particular lineages. The branch is indexed by the tree node.
Header Description
Site Character number indexed by site number of first position of the codon in the input file
Tree Tree number
SimTree Tree number for which null data was simulated (only *.null file)
Rep Replicate number
Node Node index (internal nodes only - tip nodes, branches, are labelled by the taxon name)
SYN Number of synonymous changes
NSYN Number of non-synonymous changes

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 2.0
  • MacClade