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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Too many samples on a long branch in a rooted tree containing three outgroup tips #179

Closed QianGuoPKU closed 9 months ago

QianGuoPKU commented 9 months ago

Hi,

I am building a rooted ML tree for about 1800 bacterial isolates (from a single subspecies). I set three isolates from another subspecies as the outgroup when running raxml. I want to see the ancestoral relationships within the subspecies consisting of the 1800 isolates. However, the output rooted ML tree with branch length is as below: image

As you can see the tree picture above, the three outgroup isolates were clustered in a short branch and the 1800 isolates were in a long branch. The relationships within the 1800-isolates subspecies are difficult to tell by.

I also tried to hide the branch length. The tree is below:

image

I want to visualize the topology within the 1800 isolates with the clear branchs. Do you have any ideas or suggestions?

Many thanks, Qian

amkozlov commented 9 months ago

Hi Qian,

your question is not about raxml-ng, but about general tree visualization issues. I'm not an expert in this area.

Depending on what you want to achieve, you can manually decrease the length of the outgroup branch (in the Newick file or in your tree viewer) to better see relationships between the ingroup taxa.

You can also try to use a different tree viewer, e.g. https://itol.embl.de/