User Preference
The User preference page is accessible from the Group page in SimPlot++.
There are 7 main options accessible to the user:
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Show ambiguous character warnings: Whenever a data file is loaded into SimPlot++, the sequences contained in this file are parsed to insure compatibility with SimPlot++'s features. Some characters (like the nucleic acid codes representing multiple nucleotides) could cause errors and are replaced by gaps ("-"). SimPlot++ will inform the user about these modifications through a popup dialog box. These alerts can be silenced thanks to this option.
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Automatically save SimPlot++ distance calculability report: Whenever a SimPlot analysis is performed, an HTML file containing the distance calculability report will be saved at the original file's location.
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Normalize SimPlot results: Some combinations of datasets and distance models may lead to negative similarity scores. When this option is checked, the SimPlot results will be normalized between 0 and 1.
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Save networks as svg: This option allows the user to switch between saving their similarity networks as either a .svg or .png file.
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Multiprocessing: The number of cores to use when selecting the multiprocessing feature of Simplot and BootScan analyses. The number of cores may vary between 1 and the total number of cores - 1.
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Consensus threshold: When a group contains more than a single sequence, a consensus sequence is generated. If the percentage of the most common nucleotide/amino acid type is greater then the selected threshold, then it will be added to the consensus sequence, otherwise an ambiguous character ("-") will be added to it. The consensus sequences used for most analyses in SimPlot++ can be downloaded and viewed by the user. If a more sophisticated consensus algorithm is required, we suggest using a different program in order to generate the consensus sequences.
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Gridlines: This option allows SimPlot++ to include X and/or Y gridlines in the generated plots for Bootscan and SimPlot analyses.
