Identify nodes in a phylogeny

[psorigue]

Hi,

I am using aBSREL and I obtained the already-parsed output. However, my phylogeny is very large, and I cannot identify the nodes that are named as 'node131'. Is there a way to map these nodes on the phylogeny, so I can identify what branches were under selection?

Thanks for the support

[stevenweaver]

Dear @psorigue,

You can use HyPhy Vision to view the results. There is an option to show internal tree labels.

If this is not an option for you, we also have a phylogenetic tree viewer example with internal nodes labeled here

Best, Steven

[spond]

Dear @psorigue,

Yes, indeed. There are several ways to do it.

1. The Newick tree string reported in the JSON file is annotated with node names, including internal names. . This is useful if you wish to use an external tree viewer, or annotate things programmatically (e.g. in Python)

2. You can view internal node names by loading the JSON file into https://observablehq.com/@spond/absrel as @stevenweaver suggested.

Best, Sergei

[psorigue]

Hi Sergei and Steven,

Thanks a lot for the help. I just wanted to mention that on Hyphy Vision I cannot do it (see attached image). But I will do it by using the JSON labelled nwk tree.

All the best!

[image: image.png]

Missatge de Sergei Pond @.***> del dia dj., 25 de gen. 2024 a les 14:22:

Dear @psorigue https://github.com/psorigue,

Yes, indeed. There are several ways to do it.

1.

The Newick tree string reported in the JSON file is annotated with node names, including internal names. image.png (view on web) https://github.com/veg/hyphy/assets/1018513/a87729e7-f068-4ba3-8654-200b1ad62e34. This is useful if you wish to use an external tree viewer, or annotate things programmatically (e.g. in Python) 2.

You can view internal node names by loading the JSON file into @.***/absrel as @stevenweaver https://github.com/stevenweaver suggested.

Best, Sergei

— Reply to this email directly, view it on GitHub https://github.com/veg/hyphy/issues/1683#issuecomment-1910312649, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZZAVFRR6H6BWITPBJX4ZP3YQJTA3AVCNFSM6AAAAABCKS4TU6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJQGMYTENRUHE . You are receiving this because you were mentioned.Message ID: @.***>

[spond]

Dear @psorigue,

Could you please re-upload the image directly at github? If you attach images in an e-mail response, they don't make it through.

Best, Sergei

[psorigue]

Sorry!

Here it goes:

[spond]

Dear @psorigue,

If you adjust the dimension of the plot, e.g. to 8192x800 (and click Resize), you should have enough room to see the labels.

Best, Sergei

[psorigue]

I see!

Thanks! :)

Missatge de Sergei Pond @.***> del dia dj., 25 de gen. 2024 a les 15:02:

Dear @psorigue https://github.com/psorigue,

If you adjust the dimension of the plot, e.g. to 8192x800 (and click Resize), you should have enough room to see the labels.

Best, Sergei

— Reply to this email directly, view it on GitHub https://github.com/veg/hyphy/issues/1683#issuecomment-1910387009, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZZAVFR7BIJ4SYJA6Z66KGLYQJXZBAVCNFSM6AAAAABCKS4TU6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJQGM4DOMBQHE . You are receiving this because you were mentioned.Message ID: @.***>

[psorigue]

I saw that some nodes that appear in the output, are not present in the phylogeny internal nodes. Is there a reason that I'm missing for this?

[spond]

Dear @psorigue,

Those are most likely zero-length branches which get deleted in the analysis tree for speed. The input tree retains such nodes.

Best, Sergei

[psorigue]

Ok thanks!

Missatge de Sergei Pond @.***> del dia dj., 25 de gen. 2024 a les 16:33:

Dear @psorigue https://github.com/psorigue,

Those are most likely zero-length branches which get deleted in the analysis tree for speed. The input tree retains such nodes.

Best, Sergei

— Reply to this email directly, view it on GitHub https://github.com/veg/hyphy/issues/1683#issuecomment-1910566810, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZZAVFSELL4OSRTX2MEPEY3YQKCNXAVCNFSM6AAAAABCKS4TU6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJQGU3DMOBRGA . You are receiving this because you were mentioned.Message ID: @.***>

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