What do the indices under the “pscores” command mean?
PAUP outputs several indices that measure the “fit” of characters to particular trees. The indices can be defined in terms of the following three parameters: • s= length (number of steps) required by the characters on the tree being evaluated • m= minimum amount of change that the character may show on any conceivable tree • g= maximum possible amount of change that a character could possible require on any conceivable tree (i.e., the length of the character on a completely unresolved bush). You can calculate a value for each character using the following formulae: ci= m/s ri= (g-s)/(g-m) rc= ri*ci hi= 1-c To get the overall value for a suite of characters you’ll simply caculate the sums of s, m, and g for all the charachers in the suite and use the summed values in the equations described above.
