Body: <p>These are the facts: I am working with some morphological features. Each trait can have one of the following three states: 0, 1, 2.</p>
  <p>State 0 is always independent.</p>
  <p>But if there is a trait with state 1, then there must be, in another column of the same row, a state 2 (and vice versa, obviously).</p>
  <p>The traits can't be encoded separately because, eg, in the <code>row_01</code>, at the <code>trait_01</code>, the state 1 is ligated to the <code>trait_20</code> with state 2. But in another row (<code>row_02</code>), the <code>trait_01</code> with state 1 could be ligated to another trait (<code>trait_33</code>) with state 2. My data behaves like this because I'm working with morphology in... molecules.</p>
  <p>So far, I know that the data of an array in phylogeny must be independent, so I am wondering if any of you know of any way to approach this problem (paper, algorithm, your own propose, etc.).</p>
  <p>solving conditions:</p>
  <ul>
  <li>I can't discard the traits with state 1 or 2.</li>
  </ul>
  <p>Cheers!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-06T23:50:03.827Z
Comments.Text: I am not sure that I understand. If the traits fully determine each other, why are they encoded separately? It might help to see a sample of the data. If traits were even slightly decomposable one might suggest an ordination method (like PCA) to find independent eigentraits, for example http://adn.biol.umontreal.ca/~numericalecology/Reprints/Guenard_et_al_MEE_2013.pdf.
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-06-09T04:08:25.680Z
Comments.Text: Since I last looked at this question, the editing appears to have obfuscated it. e.g. `My data behaves like this because I'm working with morphology in... molecules.` what does it mean for data to be "ligated"?
Comments.UserDisplayName: Maximilian Press
Tags: <phylogenetics>
Title: How to run a phylogenetic analysis with non-independent data?
ThreadText: # How to run a phylogenetic analysis with non-independent data?
  
  (Asked by: username_0 on 2021-06-06)
  
  These are the facts: I am working with some morphological features. Each trait can have one of the following three states: 0, 1, 2.
  
  State 0 is always independent.
  
  But if there is a trait with state 1, then there must be, in another column of the same row, a state 2 (and vice versa, obviously).
  
  The traits can't be encoded separately because, eg, in the `row_01`, at the `trait_01`, the state 1 is ligated to the `trait_20` with state 2. But in another row (`row_02`), the `trait_01` with state 1 could be ligated to another trait (`trait_33`) with state 2. My data behaves like this because I'm working with morphology in... molecules.
  
  So far, I know that the data of an array in phylogeny must be independent, so I am wondering if any of you know of any way to approach this problem (paper, algorithm, your own propose, etc.).
  
  solving conditions:
  
  * I can't discard the traits with state 1 or 2.
  
  Cheers!
  
  **Tags:** phylogenetics
  
  > **Comments:**
  > **username_1**: I am not sure that I understand. If the traits fully determine each other, why are they encoded separately? It might help to see a sample of the data. If traits were even slightly decomposable one might suggest an ordination method (like PCA) to find independent eigentraits, for example http://adn.biol.umontreal.ca/~numericalecology/Reprints/Guenard_et_al_MEE_2013.pdf.  
  > **username_1**: Since I last looked at this question, the editing appears to have obfuscated it. e.g. `My data behaves like this because I'm working with morphology in... molecules.` what does it mean for data to be "ligated"?  
  
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  ## 0 answers
  
  