These advanced options can also be used to tailor the SAPP program's calculations or output. Please be careful with these since results can be unpredictable if they are not used correctly!
When SAPP produces an output tree it shows the evolution of STR mutations along the tree branches. It can often be useful to override the default mutations along the tree branches where a user suspects that convergence has occurred or where mutations may have varied from statistical norms. This is the function of the /STRSET section. The input syntax for this section is:
NODE <nodenum> <STRLabel1> <STRValue1> <STRLabel2> <STRValue2>...
ex: NODE 30 DYS456 19 464a 15 710 13
When you first run SAPP it produces a tree showing ancestral branching points as numbered blue Nodes (e.g. "Node #35", "Node #15", etc). <nodenum> is therefore the number of the node where you want to override the STR values. The rest of the line gives the STR labels (either as long names like "DYS456" or shorthand like "456") and the new allele values to assign.
Note that you cannot override STRs in kits with this function, only higher nodes. If you wish to change the allele values in an individual kit you can simply make that correction in the /STRDATA section.
Warning: As you make other changes in SAPP (to SNPs, genealogies, etc) it will redraw the tree and reassign Node numbers to the branching points. You may need to change the <nodenum> designations to keep the overrides pointing to the right branching points.
This optional section adds to SAPP's internal knowledge of the SNP descendancy tree. By default, SAPP has an internal representation of certain major haplogroups of the known Y-SNP tree. This section allows you to add or override that tree with additional SNP branches. This can help SAPP correctly assign relationships, since it will know that two kits cannot be closely related if they are each positive for SNPs on different branches, etc.
The input syntax for this section is:
SNP1 SNP2 SNP3 SNP4 SNP5...
Ex: Z251 FGC11495 A15 ZS199
Where the format means that SNP1 is a parent of SNP2 which is a parent of SNP3 which is a parent of SNP4 and so on. To put multiple branches under one SNP, simply repeat that SNP label as the first SNP on multiple lines with each branch on its own line.
This optional section requires the use of the /STRWEIGHTS section also. By default, SAPP has an internal representation of the 111 STRs used by Family Tree DNA in the same order that Family Tree DNA uses. This section allows you to replace those STRs with a list of your own specification.
The input format is simply:
STRLabel1 STRLabel2 STRLabel3 STRLabel4...
ex: DYS456 DYS710 DYS464a DYS464b...
Either long form names or shorthand names can be used, but note that once these STRs are specified SAPP will not be able to match other forms than the ones specified (so using the example above, DYS456 must then always be referred to in the input as "DYS456", etc).
This optional section requires the use of the /STRORDER section also. By default, SAPP knows the mutation rates for the 111 STRs used by Family Tree DNA as long as its internal STR database is used. If you override that internal STR database then you must also specify the mutation rates for the new STR list you wish to use. That is the purpose of this section.
The input format is simply:
STRrate1 STRrate2 STRrate3 STRrate4...
ex: 0.0003 0.0045 0.000023 0.000018...
Note that the order of STR mutation rates must match the STR order specified in the /STRORDER section.