A julia package for phylogenetics that includes some visualization functions.
The basic tree data structure and the plot recipes are based off of NewickTree.jl
To read a tree:
tree = readnw(readline(path_to_tree))We can also root the tree automatically based on a midpoint rooting criterion (at the node which has the minimal distance to the tip that is farthest away from it):
tree_rooted = root_midpoint(tree)Trees can be clustered based on the fraction of the total divergence allowed in each subtree:
clu = cluster_tree(tree_rooted,2)Plotting is based on Plots.jl.
To plot a tree (without showing its tip labels):
plot(tree_rooted)or with tip labels:
plot(tree_rooted; labels=true)To plot the tree in an upward direction:
plot(tree_rooted; upwards=true)