Paternity analysis in Excel

Abstract

Paternity analysis using microsatellite information is a well studied subject. These markers are ideal for parentage studies and fingerprinting, due to their high discrimination power. This type of data is used to assign paternity, to compute the average selfing and outcrossing rates and to estimate the biparental inbreeding. There are several public domain programs that compute all this information from data. Most of the time, it is necessary to export data to some sort of format, feed it to the program and import the output to an Excel book for further processing. In this article we briefly describe a program referred from now on as PAE (Paternity Analysis in Excel), developed at IST and IBET (see the acknowledgments) that computes paternity candidates from data, and other information, from within Excel. In practice this means that the end user provides the data in an Excel sheet and, by pressing an appropriate button, obtains the results in another Excel sheet. For convenience PAE is divided into two modules. The first one is a filtering module that selects data from the sequencer and reorganizes it in a format appropriate to process paternity analysis, assuming certain conventions for the names of parents and offspring from the sequencer. The second module carries out the paternity analysis assuming that one parent is known. Both modules are written in Excel-VBA and can be obtained at the address www.math.ist.utl.pt/∼fmd/pa/pa.zip. They are free for non-commercial purposes and have been tested with different data and against different software (Cervus, FaMoz, and MLTR).

PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping

“…Although this study was designed to screen for low-redundancy PMSs, which do not rely on certain parentage assignment software tools, it is instructive to see if there is evidence that low-redundancy PMSs perform better with some specific software. While there are a number of tools for assigning parentage using genetic markers, we do not have many options for our testing, as most of them either used obsolete types of markers or are no longer maintained, for example, PAE [34], Sequoia [35], and FAP [36]. In particular, FAP seems suitable for our application scenario, as it can identify marker loci that are consistently associated with parental allocation errors and should be removed from the PMS.…”