TOPALi User Manual

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Legal information (licenses)

    Project files
        Creating a new project
        Opening an existing project
        Saving a project

Working with alignments
    Displaying alignments
    Summary information
    Phylogenetic overviews
    Editing alignments
        Reordering sequences
        Renaming sequences
        Replacing characters
        Removing gaps
        Restoring gaps
        Removing partition-sequences
    Display settings

Running analysis jobs
    Analysis settings
    Selecting sequences
        Basic settings
        Advanced settings
        Bambe settings
        Running PDM
        Basic settings
        Topology structure
        Model settings
        Run settings
        Running HMM
        Basic settings
        Advanced settings
        Running DSS

Working with analysis results
        PDM results
        HMM results
        DSS results
        Comparing graphs
        Adjusting settings
        Saving graphs
    Working with partitions
        Creating partitions
        Automatically partitioning
        Viewing partitions
        Selecting partitions
        Exporting partitions
        Removing partitions
    Creating Phylogenetic trees
        Selecting the data
        Creating the tree
        Viewing trees
        Grouping clusters
        Saving trees
    Predicting the mosaic structure
        Running the wizard
        Viewing the results
        Gradient shading
        Selecting colours
    Generating reports
        Selecting the result set
        Creating the report


    Checking for updates