The SAPP algorithm has been published as a scientific paper available on Academia.edu: ** (Click Here for Link). **

Below is a summary of algorithms used by SAPP. For a complete list of associated papers, please see the **Credits** section.

**Genetic Distances **use the step-wise method of counting mutations for most STRs, and infinite alleles for the "special" ones - particularly CDY, YCAII, DYS413, DYS464, DYS385, and DYS459. For STRs DYS425 and DYS439, the tool handles the occasional *null *value (represented as 'X' in the data).

This combined methodology is based on the work pioneered by Mike Walsh in administering the R1b-L21 FTDNA Project.

**TMRCA Calculations **are based on Ken Nordtvedt's Interclade Ageing methodology (his Generations67, 111, etc spreadsheets) which perform a least-squares analysis using STR differences and mutation rates to calculate the likely TMRCA ages at each branching point of the tree.

**Tree Construction **uses a neighbor-joining algorithm with three distance factors: STR off-modal signatures, genetic distance and a weighted assessment of closer STR mutation patterns using n-space vector angles. A detailed discussion of this third factor is available in this short pdf explanation.

**Tree Rendering** uses the Reingold-Tilford algorithm to draw the resulting phylogenetic tree. Credit goes to Stefan Loewe for his coding of this algorithm on GitHub.

**Other functions **are wholly the fault of the program author.