Usecase: Tree visualization with InTreeGreat
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First of all, go to this visualizator: https://phylogeny.southgreen.fr/treedisplay/index.php?data=msdmind , then follow the next steps in order to reproduce the visualization of this figure.
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Open the « Display options » menu and choose « ultrametric » in order align leaves.
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Open the « Data » menu and activate the « Polypeptide name » option. These are more informative: the last five letters indicate the species of each protein (see Uniprot species code).
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Open the « Annote branches » menu, and i) « annote all types » to collapse tree parts containing proteins that are annotated by types ; ii) choose the « color » option and iii) click on « annote all types » again in order to color the collapsed parts with colors corresponding to types. You are now in the « D » part of the figure: the compact view.
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Open the « Annote leaves » menu, and in the first section of the menu, choose « Word: Leaf ; Color: Green » then validate. Then « Word: Root ; Color: Brown », « Word: Flower ; Color: Blue » and « Word: Seed ; Color: Orange ».
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Finally, open the « Annote branches » menu and select « Collapse » option. Now, you are able to collapse / uncollapse any part of the tree, and dragging the mouse on the top of « GO / PO » you can display the full annotations of each protein. The colored squares allow you to observe correlations between the annotations and the structure of the tree.