Menu
Overview
Installation
Xml Input File
Data View
Include/Exclude Chars
Genetic Codes
Saving Data
Export Data
Tree View
Assign Branch Lengths
Rooting Trees
Print Trees
Export Trees
Output Files
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

  1. Substitution types: The number of changes from one state to another. For example, from A to C.
  2. Dwell times: The amount of time spent in a character state represented as a proportion (i.e., re-scaled such that it is the proportion of time spent in that state along the trees analyzed).
  3. Site specific rates: Typically site-specific 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

  1. Codon substitution types: The number of changes from one state to another. For example, from AGA to AGC.
  2. Codon dwell times: The amount of time spent in a character state represented as a proportion (i.e., re-scaled such that it is the proportion of time spent in that state along the trees analyzed).
  3. Amino acid substitution types: The number of changes from one state to another. For example, from I (Isoleucine) to L (Leucine).
  4. Amino acid dwell times: The amount of time spent in a character state represented as a proportion (i.e., re-scaled such that it is the proportion of time spent in that state along the trees analyzed).
  5. Omega N (dN): This is a re-scaled (by evolutionary potential) value of the number of non-synonymous changes. See here for a description of selection statistics.
  6. Omega S (dS): This is a re-scaled (by evolutionary potential) value of the number of synonymous changes. See here for a description of selection statistics.
  7. Omega (dN/dS): This is a re-scaled (by evolutionary potential) value of the ratio of dN/dS. See here for a description of selection statistics.

Morphology

  1. Substitution types: The number of changes from one state to another. For example, from 0 to 1.
  2. Dwell times: The amount of time spent in a character state represented as a proportion (i.e., re-scaled such that it is the proportion of time spent in that state along the trees analyzed).
  3. 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.
  4. 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.