flowchart.DOT

digraph flowchart {
    // default settings
    node [shape="box"];
    compound=True;

    // Nodes for algorithm
    Input [
        label="Input sequences \n (closely related sequences collections)"
    ];
    deBruijn [
        label="Generate de Bruijn graph"
    ];
    Mapping [
        label="Mapping algorithm \n from de Bruijn graph to Partial Order graph"
    ];
    PO [
        label="Obtaining the Partial Order representation"
    ];
    Extract [
        label="Extract alignment from Partial Order representation"
    ];

    // Nodes for benchmark
    Perform [
        label="Performance measures \n (Benchmark)"
    ];
    Scale [
        label="Scalability"
    ];
    Quality [
        label="Alignment quality"
    ];
    RCQuality [
        label="Row-column alignment quality measure"
    ];
    GraphQuality [
        label="Graph alignment quality measure"
    ];
    Script [
        label="Script for different algorithm auto-execution \n (with profilers)"
    ];
    Mem [
        label="Memory scalability"
    ];
    Time [
        label="Time scalability"
    ];

    // subgraph for algorithm
    subgraph cluster_algo {
        label="Whole alignment algorithm";
        labeljust=l;
        deBruijn -> Mapping;
        Mapping -> PO;
        PO -> Extract;
    }

    // subgraph for alignment quality benchmark
    subgraph cluster_quality {
        label="Different alignment quality measurement";
        labelloc=b;
        RCQuality;
        GraphQuality;
    }

    // subgraph for alignment performance benchmark
    subgraph cluster_scale {
        label="Scalability measurement";
        labelloc=b;
        Mem;
        Time;
    }

    // edges to connect nodes and subgraphs
    Input -> deBruijn;
    Extract -> Perform;
    Perform -> {Quality, Scale};
    Quality -> {RCQuality, GraphQuality};
    Scale -> Script;
    Script -> {Mem, Time}
}