The SAPP algorithm has been published as a scientific paper available on Academia.edu: (Click Here for Link).
The following papers were used in the design and development of the SAPP program:
Walsh B. Estimating the time to the most recent common ancestor for the Y chromosome or mitochondrial DNA for a pair of individuals. Genetics. 2001;158(2):897-912.
Gascuel, O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol (1997) 14 (7): 685-695.
Bruno, William J.; Socci, Nicholas D.; Halpern, Aaron L. Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction. Mol Biol Evol (2000) 17 (1): 189-197.
Saitou, N.; Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 4 (4): 406-425.
In addition, the following people knowingly or unknowingly contributed their expertise to the development of this program:
... and many more of the experts!