FPG Software

Description

FPG stands for "Full Parental Genotyping." That is the name we have given to efforts underway to develop a panel of SNPs to be used for very large scale parentage inference in hatchery populations of salmon. Currently this software suite consists of two C programs and a number of scripts.

The two C programs are:

  • snpSumPed - a program that computes the probability of configurations of SNP genotypes on trios of individuals which are related in ways specified by the user using a combination of pedigree links and pairwise relationships.
  • TrioTests - a program that employs an importance sampling algorithm that can be used to compute false positive and false negative rates for doing parentage inference. This program requires input from snpSumPed in order to work.

The scripts simplify the use of the above two programs.

Software

Download files include the source code for the two C programs and a directory of scripts and associated pedigree files.  An extensive tutorial is also provided, describing how to use the programs and scripts.  It is assumed that the user is familiar with the Unix environment.

Current version: 1.0
Release date: 30 May 2006

Documentation

The software accompanies the following journal article:

Anderson, EC and JC Garza (2006) The power of single-nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567-2582.
[view online The previous link is a link to Non-Federal government web site. Click to review NOAA Fisheries disclaimer ]

Registration

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:

  • name
  • email address
  • affiliation
  • how you plan to use the program

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Last modified: 12/24/2014