Hello,
I am facing the following situation:
I have two species phylogenies of groups very distantly related to each other. For each tip (species) I have the value for a continuous trait. I would like to check whether or not there is a significant difference between the two groups, while accounting for within-group relatedness.
AFAIK, this type of analysis is usually done with a phylogenetic ANOVA test, e.g. as implemented in the R package phytools. However, the function expects a single phylogeny, not two.
Can anyone suggest a software that can do what I need, or help me think of a procedure for performing the analysis?
Thanks!
Hello professor Glick
I’m not sure about your problem but if you want to detect a value that is different between your species and the value is a continuous trait, you probably can use this.
You can set one data frame for each species. For example, in data frame A, the column will include the samples(name or ID or ...) and the row will include their unique value for each continuous trait
data frame A (color blue)
[sample 1, value A1 value B1 and …
sample 2, value A2 value B2 and …
....
data frame B ( color red)
[sample 1, Value A1, value B1 and ...
...
then you should display each value with a specific color Blue or Red
For example, in value A, most of the blue colors are …. (Type of value) And the reds are ….
Then you can check and understand what is the type of each value in each species and detect the significant differences between them. Moreover, you can apply different conditions to your data set. Here is an example, you can only display a value that has more than 80% similarity in each species but is different compared to other types. Also, if you don't need to display it as a graph, you can use a simple code with the Pandas library in python to detect the significant values and their types. I don’t know what are the types of your value but I hope I understand your problem correctly and this will help you
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