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Substitution Models
Morphology Priors
Analysis (Mapping)
Mapping Statistics
Analysis (Correlation)
Correlation Statistics
Analysis (Selection)
Selection Statistics
Analysis (ASR)


Mapping Statistics
SIMMAP 1.5 can summarize each individual mutational map using a variety of statistics  these are identical to the summary statistics which are the posterior expectation (or mean) of these values. See here for a description of how to configure a mutational analysis to collect these statistics to a file. The statistics described below are by data type.
Nucleotides
 Substitution types: The number of changes from one state to another. For example, from A to C.
 Dwell times: The amount of time spent in a character state represented as a proportion (i.e., rescaled such that it is the proportion of time spent in that state along the trees analyzed).
 Site specific rates: Typically sitespecific rates (e.g., the discrete gamma of Z. Yang) model rate variation as a distribution that is the best fit averaged across all sites. This statistic reports the values sampled from this distribution and represent the posterior distribution of rates for a particular site, conditional on the parameter of the gamma distribution.
Codons
 Codon substitution types: The number of changes from one state to another. For example, from AGA to AGC.
 Codon dwell times: The amount of time spent in a character state represented as a proportion (i.e., rescaled such that it is the proportion of time spent in that state along the trees analyzed).
 Amino acid substitution types: The number of changes from one state to another. For example, from I (Isoleucine) to L (Leucine).
 Amino acid dwell times: The amount of time spent in a character state represented as a proportion (i.e., rescaled such that it is the proportion of time spent in that state along the trees analyzed).
 Omega N (dN): This is a rescaled (by evolutionary potential) value of the number of nonsynonymous changes. See here for a description of selection statistics.
 Omega S (dS): This is a rescaled (by evolutionary potential) value of the number of synonymous changes. See here for a description of selection statistics.
 Omega (dN/dS): This is a rescaled (by evolutionary potential) value of the ratio of dN/dS. See here for a description of selection statistics.
Morphology
 Substitution types: The number of changes from one state to another. For example, from 0 to 1.
 Dwell times: The amount of time spent in a character state represented as a proportion (i.e., rescaled such that it is the proportion of time spent in that state along the trees analyzed).
 Bias rate: The bias rate is the analogous to the state frequencies of nucleotide models. This represents a prior model on morphological/standard characters. A number of different priors can be used depending on the number of character states. For characters with two or more (the minimum number of states required for a character) states an equal and empirical prior can be chosen. For characters with two states you also have the option of a fixed prior or a Beta distribution prior. For more information on configuring models see here and for more on morphology priors see here.
 Overall rate: This is prior model on the the overall rate of a character change. (This is a multiplier of the underlying branch lengths used in the analysis.) This parameter can be implemented in a number of ways: fixed value, branch length values (1.0), and using a discrete gamma distribution.
