Best way to visualize large phylogenetic trees

Question

[hakon.kaspersen]

I am currently creating phylogenetic trees in R to visualize and annotate them. When working with this, I realized that, due to the relatively high amount of isolates (just under 300), the trees tend to get quite big and hard to read. The lines get jumbled up into eachother, and the nodes get too small to read. This is the case for both circular and rectangular trees.

So after looking at this, I though of other ways to visualize the phylogenetic relationships between these isolates, but I can't seem to find anything useful. Is there a way to use, for example, PCA or NMDS? Some other clustering method?

What I would like to do is to use the distance data to visualize the phylogenetic relationship in another way, perhaps more compact, than dendrograms.

Any thoughts?

[Joe]

Can you just collapse some nodes in to sensible clusters?

Answer 1

[Mensur Dlakic]

You may want to check out the interactive tree of life. It is meant for big trees and you can test different representations easily.

It is very difficult to make a legible tree with 300 nodes, especially if you have long names on top of that. If you don't need all of them, or if some are near-identical, I would consider removing some. Yet another option is to collapse branches together. Most interactive tree programs have an option to do it. Among programs that are specifically meant for big trees, I suggest archaeopteryx.

[Mensur Dlakic]

For an alternative way to visualize phylogenetic relationships as clusters, see here and here.