Workload examples - arklumpus/TreeViewer GitHub Wiki

This page contains tutorials on how to perform some common workloads in TreeViewer.

[Drawing a tree highlighting support values]]: this tutorial shows how to re-root a tree and draw it so that nodes with very low support values are collapsed and the support value for other nodes is highlighted by a circle on the node. ](/arklumpus/TreeViewer/wiki/<p-align="center"><img-src="Thumbnails/CharacterStates.png"-width="256">-[[Displaying-character-states-on-a-tree): this tutorial shows how to display character states along with the phylogeny.	Displaying BLAST scores: this tutorial shows how to highlight BLAST scores (or any other kind of score) on a tree.
[Working with large trees from the command‐line interface]]: this tutorial provides an example of how TreeViewer can be used to plot huge trees using the command-line interface. ](/arklumpus/TreeViewer/wiki/<p-align="center"><img-src="Thumbnails/Images.png"-width="256">-[[Drawing-taxon-images): this tutorial shows how to include taxon illustrations in a phylogenetic tree plot to highlight the kind of organisms that are represented.	Drawing an alignment with the tree: this tutorial shows how to draw an alignment together with the tree in order to highlight sequence features.
[Plotting the age distributions in a time‐calibrated tree]]: this tutorial shows how to plot the age distributions when a posterior sample from a Bayesian molecular clock analysis is available. ](/arklumpus/TreeViewer/wiki/<p-align="center"><img-src="Thumbnails/MultiAgeDistributions.png"-width="256">-[[Plotting-multiple-age-distributions): this tutorial shows how to plot multiple age distributions on a single tree, e.g. to compare prior and posterior estimates.	Plotting the results of a stochastic mapping analysis: this tutorial shows how to plot the results of a stochastic mapping analysis, showing the posterior probability of different character states along the tree branches.
[Creating a new tree]]: this page contains information on how to use TreeViewer to create a new random tree or to build a tree using biological data. ](/arklumpus/TreeViewer/wiki/<p-align="center"><img-src="Thumbnails/CropRegions.png"-width="256">-[[Crop-regions-and-output-DPI): this tutorial shows how to define crop regions to export only a part of the tree plot, and how to set the output resolution for raster image formats (PNG and TIFF).	Tree statistics: this page contains information about how to compute and interpret tree statistics in TreeViewer.
	Comparing trees: this tutorial shows how to compare a tree with another tree or with multiple other trees.