SNPPIT is a program for performing fast and accurate, likelihood-based, parentage inference with single nucleotide polymorphisms (SNPs). The software is tailored for inference of mother-father parent pairs, not for single parents. It takes a simple input file that includes the genotypes of the possible parents and of the offspring whose parentage is to be inferred. Parents in the parent database may come from multiple populations. This program was developed for massive-scale parentage inference of hatchery produced salmon and can accommodate hundreds of thousands of parents in the parent database. There is also the option to include metadata for each individual that might be available with hatchery salmon, like spawning date, spawning year, age range of offspring, etc.
The archive below includes source code and compiling instructions as well as pre-compiled binaries for Windows and for Mac OS X. It also includes a technical report that describes the statistical method, provides documentation on how to use the program, and sample data files.
Software archive: SNPPIT 1.0 (1 MB zip file)
This software accompanies the following report submitted to the international Pacific Salmon Commission's Chinook Technical Committee (US Section). The report is also included in the software archive above.
Anderson, Eric C.
2010. Computational algorithms and user-friendly software for parentage-based tagging of Pacific salmonids. Final report submitted to the Pacific Salmon Commission's Chinook Technical Committee (US Section). 46 p.
Software registration is optional. However, we like to know who is using it and for what purpose so that we may develop our software in a manner that is useful to you. Your information will not be distributed to anyone else.
To register, send an email to Eric Anderson with the following information:
- email address
- how you plan to use the program