ggtree visualization different from dendroscope visualization

YuLab-SMU / ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees

https://yulab-smu.top/contribution-tree-data/

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ggtree visualization different from dendroscope visualization #345

Open limin321 opened 4 years ago

limin321 commented 4 years ago

Prerequisites

Hi, I created a phylogenetic tree from whole genome ANI values 0f 300 strains. When I visualized the tree using ggtree, it had polytomy branches while it was opened in dendroscope, all branches were double lineages.

Does anyone have any suggestions what might cause this difference?

Really appreciate your help.

Best, Limin

brj1 commented 4 years ago

I'm not super familiar with dendroscope, but it's possible that dendroscrope does not display the tree scaled by edge length. If there are really short edges in your tree they may appear as polytomies in ggtree. Try the following code which will make the branch lengths the same:

ggtree(tree, branch.length = 'none')