User Preferences
By loading a file either in the climatic process, you'll be able to generate a tree. By clicking on the Tree button, you will be able to select some parameters which will change the rendering of the tree.
Esthetic parameters (for the network view):
- Label color: change the color of the label displaying the species name.
- Edge color: change the color of the edge of the connexions.
- Reticulation color: change the color of the knots between the species.
Layout parameters (for the network view):
- Hierarchical Vertical / Horizontal: keep the classic tree layout but it can be shown horizontally or vertically.
- Axial layout: generate a layout based on an axial symmetry pattern.
- Radial layout: generate a layout based on a circular pattern.
Visualization parameters:
- Network view: visualize the connexions as a network or a spider web.
- Tree view: classic phylogenetic tree visualization.
- Proportional edges length: modify the lengths to be proportionally accurate.
- Show branches length: display the length of the branches.
- Use leaf names: use and display the names used in the previously uploaded file.
Once both process are done loading a file, you will be able to generate results based on both genetic and climatic data manipulations. The Settings button permits to choose how to display the results and which method the algorithm will use to generate the results tab.
Calculus method:
- Least Square distance: this method will adapt the distance based on the similarity rate between the species.
- Robinson-Foulds distance: this method will maintain an equal distance between all the branches.
- Euclidian distance: this method will maintain an equal distance between two interconnections.
Threshold selection:
- Bootstrap threshold: the higher the bootstrap, the higher repetitions are done before rendering the tree.
- Metric threshold: the higher the metric threshold, the more reliable the results will be.