SIMMAP | output files

Output Files

This help page provides information on the format and contents of the different output files generated by SIMMAP. Details on how to save the different files is covered elsewhere and links are provided for further reading.

The next section describes the specifics of each type of file. All of the files are tab-delimited text files except the tree files and modified data files. Most of the files contain a single line at the start identifying that file came from SIMMAP, the version number, and the date and time. For example,

[SIMMAP 1.0 Beta 2.0 : Tue 03/14/06 01:44 PM].

Specifics on each file type:

Individual Statistics File
Statistics collected during an analysis of posterior histories. These values can only be saved during sampling unlike the summary statistics (see below). The following are the tab-delimited column's contents (not in the order they appear in the file):

Summary Statistics File
Summary statistics collected during an analysis of posterior histories are reported as the posterior expectation. Summary values are continuously collected and may represent summary over multiple analysis runs. To avoid combining data inappropriately values can be cleared between runs and saving. These values can be saved during sampling or after sampling is complete. For more information see the help pages on molecular statistics or morphological statistics. The following are the tab-delimited column's contents (not in the order they appear in the file):

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. The node indices for each tree can be viewed by selecting Display Tree Node Indices from the Trees main menu. Node indices can not be viewed when a character history is being shown. The option to save these statistics is only available through the use of predictive tests (more information on predictive tests can be found here) and therefore two files with the headers and column contents listed below are saved: (1) the observed values (*.obs) and (2) null or predictive values (*.null). A note of caution: These files can become very large in size depending on the number of species, number of replicates, and number of sites requested. It is recommend you test how big the files will be before performing a full analysis. If the size is very large it is recommended that you split the analysis into multiple runs. The following are the tab-delimited column's contents (not in the order they appear in the file):

Tree Histories File (Raw character histories)
In addition to the statistics described above the details of each individual history can be written to a file as a tree history (continuous character map).The following is an example of a character history for a three taxon tree represented in SIMMAP's modified Newick tree history format:

((Taxon1:{A,0.1:C,0.1},Taxon2:{T,0.1:C,0.1}):{C,0.1},Taxon3:{C,0.4})
For a detailed description of raw character histories see the help page on tree histories.

Summary Trees
SIMMAP offers the option to save the number of changes along particular branches of the phylogeny to a tree file. Users can opt to save molecular changes in the following way (morphological characters are simply the number of changes). For the details of activating these options see the appropriate section in the help page on menu options.

Options are available for molecular data:

Save nucleotide changes as branch lengths
- Nulceotide changes are saved as the number of changes for each realization.
Save amino acid changes as branch lengths
- Amino acid changes are saved as the number of changes for each realization.
Save codon changes as branch lengths
- Codon changes are saved as the number of synonymous and non-synonymous changes for each realization. Seperate trees for each type of change are saved.

The output file is a standard NEXUS tree file containing a translate block followed by the trees. The following are examples of a single tree saved for each data type.

Morphological Characters

tree utree[4,1,2,0.5453,3.1522] = ((Taxon1:0.0,Taxon2:2.0):1.0,Taxon3:0.0);

The values contained in the square brackets following utree are as follows: character number, tree number, number of character states, bias parameter (for characters with more than 2 states this value is 1/k states), and the overall evolutionary rate (gamma rate value).

Molecular Characters - Nucleotides

tree utree[3,nuc] = ((Taxon1:1.0,Taxon2:0.0):0.0,Taxon3:1.0);

The values contained in the square brackets following utree are as follows: character number and data type (nucleotide in this case).

Molecular Characters - Amino Acid

tree utree[4,amino] = ((Taxon1:1.0,Taxon2:0.0):0.0,Taxon3:1.0);

The values contained in the square brackets following utree are as follows: character number (referenced to the character number of the first nucleotide position of the codon) and data type (amino acid in this case).

Molecular Characters - Codons (Synonymous and Nonsynonymous)

Codon changes are saved as the number of synonymous and nonsynonymous changes. A tree for each type is changed for a single character history.

tree utree[4,syn] = ((Taxon1:1.0,Taxon2:2.0):0.0,Taxon3:1.0);
tree utree[4,nsyn] = ((Taxon1:1.0,Taxon2:0.0):0.0,Taxon3:0.0);

The values contained in the square brackets following utree are as follows: character number (referenced to the character number of the first nucleotide position of the codon) and data type (synonymous and nonsynonymous in this case).

Saving Trees to NEXUS file
If the trees in memory have been modified (e.g., by pruning taxa from them or by assigning birth-death branch lengths) they can be saved to a standard Nexus file in the Newick format.

Modified Data Matrix
SIMMAP offers the option to save the data matirx in different formats. For details on these options see the help page on saving the data matrix.

Page Last Updated: 6 August 2008

	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

	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

	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


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