Bipartition question

[richardgoater]

Hello, thanks for a nice library!

I'm trying to implement a neighbour-joining example and I come across this issue on the penultimate step:

+---------- F                                                                             
|                                                                                         
|          +--------------------------------- E                                           
|----------|ED                                                                            
|          +---------------------- D                                                      
|                                                                                         
|                                 +---------- B                                           
|          +----------------------|BA                                                     
+----------|BAC                   +-------------------------------------------- A         
           |                                                                              
           +---------- C                                                                  

--- FAIL: TestNJ (0.00s)
panic: We cannot add the bipartition, it already exists [recovered]

It is attempting to join F and ED at this point. Can I detect this situation and do something different perhaps?

[fredericlemoine]

Hello, Could you provide a small example of the way you call the function? Thanks, Frederic

[richardgoater]

Thanks for the quick reply @fredericlemoine, I think this line is the one of interest: https://gist.github.com/richardgoater/867546a4ec48cc75e570f1f42deb79ff#file-nj-go-L85

I realise that I'm not checking for errors with the edges on lines 77-78.

EDIT: Added a test file to the gist

[fredericlemoine]

Hello, Wouldn't it be due to the fact that your tree is already fully resolved? It seems there is no "polytomies" left, i.e nodes with more than 3 neighbors. By the way, there is a function you can call to create a startree from taxa names directly:

t,err := tree.StarTreeFromName(taxa...)

[richardgoater]

Thanks for your thoughts, and thanks for the tip on creating the startree. I think there should be one more round of joining at this point, the matrix is 3 x 3 with nodes F, ED, and BAC. The implementation is probably not 100% correct, and I still need to implement the final operation when the matrix is 2 x 2.

[fredericlemoine]

Ok, but I don't think you can add a new bipartition, as all the internal nodes have already 3 neighbors. Are you sure you need a 2x2 matrix? (see here for example)

[richardgoater]

Thanks again, is there something else I can do instead of a bipartition? I've been following this example: http://www.evolution-textbook.org/content/free/tables/Ch_27/T11_EVOW_Ch27.pdf I believe the program is stuck at cycle 4, and I need to implement the "final step" here: https://gist.github.com/richardgoater/867546a4ec48cc75e570f1f42deb79ff#file-nj-go-L107

[richardgoater]

Hi, I think I have it working now and updated the gist. I realised I just need to assign distances to the existing nodes in the situation above (and I was also assigning distances the opposite way round, now fixed). Thanks very much for your time again, and thanks for the library.

[fredericlemoine]

Thanks for the update