Xml Input File
Assign Branch Lengths
SIMMAP 1.5 can generate a number of different output files depending on the type of analysis and the output options selected. Each subsection below details some basics of the output files. Some of these sections refer you to other help pages that provide the needed details.
The data can be modified in the the Data View window. More details can be found here.
The data loaded into SIMMAP 1.5 can be exported in a number of formats. More details can be found here.
The trees loaded into SIMMAP 1.5 can be exported in two different formats. More details can be found here.
Save Individual Statistics:
When performing a mutational mapping analysis individual statistics for each replicate can be saved to a file. To save the individual statistics open the Analysis window and select the General tab (Figure 1).
In the Output/Results box select Save individual statistics to file and then select a a fine name and location.
The next step is to select the specific statistics to be collected and saved. Select the Statistics tab and check/un-check the statistics desired. By default all of the statistics will be reported.
These statistics only apply to mutational mapping analysis. Statistics for the analysis of correlation (association) and positive selection are always active. Details of the correlation statistics can be found here and for the positive selection analysis here.
Save Summary Statistics:
Summary statistics, i.e., the posterior expectations, can be saved to a file during the analysis or after the analysis from the Summary Statistics window.
To save the summary statistics during an analysis select General tab in the Analysis window (Figure 1) and in the Output/Results box select Save summary statistics to file and then select a a fine name and location. Next select the Statistics tab and check the statistics desired (Figure 2).
To save the summary statistics after an analysis open the Summary Statistics window by selecting Statistics->Data Type->Summary Statistics... (Figure 3).
Select Save Results and choose a file name and location. This saves the summary statistics for all characters/sites shown in the table.
Save Mutational Maps:
Each mutational map generated during an analysis can be saved to a file. This permits further analysis or display of the mutational histories later. To save mutational histories open the Analysis window and select the General tab (Figure 1).
In the Output/Results box select Save mutational maps to file and then select a a fine name and location.
Mutational maps are saved in a Newick tree format (in a Nexus formatted file) with the mutational history embeded as a comment before the branch length. For example:
Mutational states are coded as integers (0 = A, 1 = C, 2 = G, 3 = C). The last state does not have a length associated with it as its length can be obtained from the difference in the branch length and the sum of the other mutational intervals.
When mutational maps are saved during a correlation analysis, codon mutational mapping analysis, and positive selection analysis the states are written as alphabetic characters (e.g., AAC, AC, 01, etc...).
Each tree is labelled with different information about the analysis. See below for the naming conventions for each type of analysis (values shown as 0 are numeric values such as the tree number, etc.):
- Nucleotide, fixed model - utree.t0.c0.r0
- Nucleotide, model parameters from file linked to a tree - utree.t0.c0.r0
Save Predictive Statistics and Mutational Maps:
Two analyses use predictive simulations to determine statistical significance: character correlation (association) and positive selection.
During these analyses and when Predictive Simulations are activated the statistics and predictive expectation can be saved. To access these options select Sampling tab in the Analysis window (see Figure 4 below).
To save the predictive mutational maps during an analysis select the Save predictive maps to file checkbox and then click the Set button and choose a filename and location to save the output.