text: user2961: To calculate the retention index for a phylogenetic tree, we use the following formula:
  $$\frac{\text{maximum number of steps on tree - number of steps on the tree}}
  {\text{maximum number of steps on tree - minimum number of steps in the data}}$$
  To calculate the maximum number of steps, we look at the number of observed character states for a character and take the lowest number. For each character, we take the lowest number of observed traits and then sum across all characters.
  Take the following dataset (columns are characters, taxa are rows):
            123456
  Outgroup  000000
  Taxa A    100001
  Taxa B    110001
  Taxa C    111001
  Taxa D    111101
  Taxa E    111111
  Taxa F    111110
  
  The maximum number of steps for the first character is 1, since the character state 0 is attested once and character state 1 occurs six times. 
  What I don't understand is why we do not use 6 for the maximum number of changes for the first character. 
  
  user181: The maximum number of steps (or changes) is the number of taxa with state 1 or 0, whichever is smaller. Conceptually, this is the number of character changes if each taxon evolved its state independently of the other taxa. 
  If for a given character the character state 0 occurred twice and character state 1 occurred five times, 2 would be the maximum number of changes.
  
original_text: 2961: <p>To calculate the retention index for a phylogenetic tree, we use the following formula:</p>
  
  <p><span class="math-container">$$\frac{\text{maximum number of steps on tree - number of steps on the tree}}
  {\text{maximum number of steps on tree - minimum number of steps in the data}}$$</span></p>
  
  <p>To calculate the maximum number of steps, we look at the number of observed character states for a character and take the lowest number. For each character, we take the lowest number of observed traits and then sum across all characters.</p>
  
  <p>Take the following dataset (columns are characters, taxa are rows):</p>
  
  <pre><code>          123456
  Outgroup  000000
  Taxa A    100001
  Taxa B    110001
  Taxa C    111001
  Taxa D    111101
  Taxa E    111111
  Taxa F    111110
  </code></pre>
  
  <p>The maximum number of steps for the first character is 1, since the character state 0 is attested once and character state 1 occurs six times. </p>
  
  <p>What I don't understand is why we do not use 6 for the maximum number of changes for the first character. </p>
   181: <p>The maximum number of steps (or changes) is the number of taxa with state 1 or 0, whichever is smaller. Conceptually, this is the number of character changes if each taxon evolved its state independently of the other taxa. </p>
  
  <p>If for a given character the character state 0 occurred twice and character state 1 occurred five times, 2 would be the maximum number of changes.</p>
  