Probability of Synapomorphy

Probability of Synapomorphy was designed as an R script that implements a new method for evaluating synapomorphy on phylogenetic trees.

All you have to do is install R and run the script. A method that quantifies the pattern of character state distribution over a cladogram and as such is free of any transformational model.

The condition is defined for a fully synapomorphic character state as a character state shared by all of the clade’s terminal taxa and at the same time completely absent from all terminal taxa outside that clade.

The extent to which this condition is not violated serves to quantify the probability of synapomorphy. This probability is calculated as a combination of relative character state frequencies within and outside the clade based on the hierarchical structure of the cladogram.

It corresponds to the probability of randomly selecting two terminals that share the same character state within the clade and at the same time differ from all outside terminals.