I'm trying to show the gene trees discordance with toytree. But the cloud tree I got is quite different with given fish example.
To figure out the problems I met, I decline the number of trees used to plot cloud tree.
And I find the leaf branches of trees in cloud tree are not aligned ! But I cann't find the parameter to change it.
The trees were generated by FastTree with default parameters based on the protein sequences. And the draw_cloud_tree code is shown below:
mtrees = toytree.mtree('/ldata/gujianhui/Ortho_analysis/Poaceae/OrthoFinder/Results_May02/Orthogroups/busco_genes/busco_trees')
rooted_tree = toytree.mtree( [ i.root( 'Ananas_comosus') for i in mtrees.treelist ] )
con_tree = rooted_tree.get_consensus_tree()
rooted_tree.draw_cloud_tree(
fixed_order= con_tree.get_tip_labels(),
tip_labels_style={"font-size": "11px"},
);
If you can give me any suggestions at your convenience, I'd appreciate it!
I'm trying to show the gene trees discordance with toytree. But the cloud tree I got is quite different with given fish example.
To figure out the problems I met, I decline the number of trees used to plot cloud tree.
And I find the leaf branches of trees in cloud tree are not aligned ! But I cann't find the parameter to change it.
The trees were generated by FastTree with default parameters based on the protein sequences. And the draw_cloud_tree code is shown below:
If you can give me any suggestions at your convenience, I'd appreciate it!