gl.tree.nj - missing values error

[Dallas]

Hi there,

I'm trying to create a phylogenetic tree with my genlight object using the following code:

ph.tree <- gl.tree.nj(gl_complete, type="fan")

ph.tree

But I get the error: Error in ape::nj(d) : missing values are not allowed in the distance matrix Consider using njs()

I can't figure out how to remove the missing values it's talking about from my genlight object. I used gl.tree.nj with the testset.gl, and it worked. I looked into njs(), but it seemed more complicated than just removing the missing values.

Thanks!

Dallas

[Arthur Georges]

Not sure what is going on there Dallas. The testset.gl has lots of missing values, so I suspect that the issue is that one or more of your entities has missing values for all attributes. Perhaps you could try

D <- dist(gl)

D

to see if that is the issue.

BTW the neighbour joining tree gives a tree representation of genetic similarity, not really a phylogeny.

Arthur

[Dallas]

Hey Arthur,

I ran the code you gave on my genlight object, but am unsure what I should be looking for? I didn't get any errors when I ran it.

Dallas

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[Arthur Georges]

You are looking at the distance matrix to see if there are any NA's in there, as these could be causing the issues that you observed. :)

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