Phylocom non-ultrametric tree vs ultrametric tree

Question

Again.

I need help one more time.

Nowadays I am getting into PHYLOCOM software for inferring characteristics of a phylogeny from different samples. This software allows you to calculate if your species are showing clustering or overdispersion within other populations in your analyses. As input files you need a phylogenetic tree in NEWICK format and a sample file (.txt).

I have done two tests, one modifying my tree in R with 'ape' package this way:

compute.brlen(tree, main=expression(rho==10))

And the other one by this other 'ape' option:

tree$edge.length = tree$edge.length * 10

The first modification generates an output with an ultrametric tree while the second output is a non-ultrametric tree. If then I run PHYLOCOM itself by

phylocom comstruct

I get different results, not only in the values of the parameters, but also in the signification p-values.

My question is if anyone knows how should I run the PHYLOCOM to do these 'comstruct' analyses correctly, with an input of a ultrametric or non-ultrametric, and also what are the differences in running this in oone way or in another.

I know this is not a 'classical' question for stackoverflow forums, but maybe anyone that works with phylogeny could help me.

Thanks a lot.

Answer 1

I think I may be able to help, but unfortunately I cannot add comments to get more information so I will have to infer what you mean from the information given. I apologize if it doesnt help.

Firstly, you may want to consult the help for compute.brlen(). As there is no argument for "main" in this function. I think you have taken it from the example in the help file, but you may note that this is outside the compute.brlen function and in the plot function. It will give you a title in your plot.

To change the rho value in compute.brlen() you need to change the power argument. For example:

compute.brlen(tree, power = 10)

This may be why you are getting different results for the different trees. Because there is no transformation being performed on your compute.brlen() tree.

I am not familiar with PHYLOCOM, so I can't help on that front. But ultrametric and non-ultra-metric trees will give different relationships between the tips of the tree, so I would not be surprised that they give different results. I should note that I am not super confident on the differences in the analysis of ultrametric and non-ultrametric trees, but from looking at the plotted differences I would assume that this is true.