Features

MACH2 Features

MACH2 infers migration histories of metastatic cancers given the clonal phylogeny and the location of extant clones.

MACH2 takes as input the following:

1. Input tree file : Tree file describing the input clone tree.
2. Leaf labeling file : Labeling file describing the leaf labeling of input clone tree.

And returns output in one of the following formats:

1. Refined tree file : Tree file describing the output refined tree.
2. Vertex labeling file : Labeling file describing the vertex labeling of the refined tree. Labels designate the anatomical location of each node.
3. Refined tree DOT : Refined tree with vertex labeling in DOT format.
4. Migration graph file : Multi-graph file describing the migration graph.
5. Migration graph DOT : Migration graph in DOT format.

MACH2-Viz Features

MACH2-Viz is an interactive visualizer that allows the user to explore migration patters inferred by MACH2. It has the following features.

• Highlight corresponding nodes: The user can highlight nodes in the clonal tree or migration graph, and nodes in the corresponding structure will highlight as well.
• Compare solutions: Users can open solutions side by side and compare them.
• Require or omit migrations: A summary panel can be opened and migration edges can be required or omitted from the list of solutions displayed.
• Examine polytomy refinement: The input clonal phylogeny can be compared against the refined phylogeny and corresponding nodes can be panned to and comapred.
• Extensibility: Users can upload their own solutions or make contributions to the home page table of example solutions.
• Backwards compatibility: Solutions from MACHINA (2018) can also be loaded into the visualizer.