8000 Species tree not binary but appears to be binary in figtree · Issue #204 · bpp/bpp · GitHub
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Species tree not binary but appears to be binary in figtree #204

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ngripshover opened this issue Jan 15, 2025 · 5 comments
Open

Species tree not binary but appears to be binary in figtree #204

ngripshover opened this issue Jan 15, 2025 · 5 comments

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@ngripshover
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ngripshover commented Jan 15, 2025 •
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I am having trouble running the A11 species delimination tree. I was able to run the example files but using my own data is causing an issue.
My tree appears to be binary but I am recieving the error message: "Species tree is not binary".
Here is my newick tree for the species tree and I have attached the figtree output of this newick tree format:

(G_ca, (S_fr, ((S_se, S_ep), (S_at, (((T_boc, T_cal), T_ceb),(T_oax, (((T_ver, T_arm), T_mel),((((((((((T_tae, T_imp), T_sla),T_rub), T_sup), T_cuc), (T_can, T_lin)), T_sch), T_alt), (((T_wil, ((T_cor, T_rel),((T_pla, T_yaq),((T_hob, T_gra),(T_atr, T_nig))))))))))))))));

Screen Shot 2025-01-15 at 2 37 32 PM

Could anyone help me solve this problem?
@ziheng-yang
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there is a trifurcation in the middle.
please post questions at the bpp discussion group.
here the github site is mostly for reporting bugs.
best wishes,
ziheng

@ngripshover
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I apologize for posting here. Where is the bpp discussion group?

@ngripshover
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Ziheng,

I've tried to run a smaller tree to figure out the issue using this newick tree. It runs with this:
(G_ca,(S_fr,((S_se,S_ep),(S_at,(T_ceb,(T_boc,T_cal))))));

Image

But when I add another species and adjust the parenthesis, I receive the species tree not binary in the "Summary of alignments after phasing sequences" and the program stops running.
(G_ca,(S_fr,((S_se,S_ep),(S_at,(T_ceb,((T_boc,T_cal),(T_oax)))))));

Image

I do no understand why bpp is saying this in not binary format when each node has only two branches?

@xflouris
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Hi @ngripshover ,
the tree contains an unary node, i.e. an inner node with only one descendent. Towards the end of the newick string there is:
(T_oax)
that's the unary node - an inner node with just one descendent T_oax. Delete the parenthesis around T_oax to fix it, i.e.
(G_ca,(S_fr,((S_se,S_ep),(S_at,(T_ceb,((T_boc,T_cal),T_oax))))));

@ngripshover
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If anyone else runs into this issue, I used the program mesquite to create a tree and then exported the tree in newick format to use as my starting tree if bpp.

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@xflouris @ziheng-yang @ngripshover
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