Phylogenetic methods question: how would you build a tree from categorical data that is polymorphic within species, but you know the frequencies of the morphs?
I.e. for this character, there are state 0 and 1, but in species A, state 0 occurs 30% and in species B 60%. For that character, there are states 0, 1, and 2. species A has 0 at 23%, 1 at 38%, and species B has 0 at 39% and 1 at 21%. Etc.
Maybe you could explore constructing it in BEAST, it can deal with trait data (even including continuous values) :
https://beast.community/continuous_traits
I have some blog regarding phylogenetic tree construction, this might help in some way... albeit it for beginners...
here is the link...
https://hubpages.com/education/DNAge-Molecular-Dissection-of-Species-Identity
Rutger A. Vos please find the following link, I hope some little help to you.
https://www.jstor.org/stable/2413656?seq=1
Benefits of phylogenetic classification is immense. They direct searches for useful genes and act as the most efficient framework for communication, so as to link all fields of biological taxonomy. They also establish a framework for measuring extinction rates and the processes of speciation and adaptation which are responsible for the present day biodiversity.
You can have a look at this link as well- https://link.springer.com >chapter
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