Relatedness Estimation and Rarefaction Analysis Tool (RE-RAT)

Introduction

Relatedness Estimation and Rarefaction Analysis Tool (RE-RAT) is a web-based tool for calculation of microsatellite-based pairwise relatedness estimates and for the execution of rarefaction analyses to determine the number of loci needed to provide stable estimates of relatedness. RE-RAT was originally developed by Lori Schwacke and Patricia Rosel of the National Oceanic and Atmospheric Administration (NOAA) as a tool for performing rarefaction analyses and testing relatedness hypotheses for populations of small cetaceans. A web-based interface has now been added so that RE-RAT is easily accessible from a variety of platforms and is being made freely available to the scientific community.

RE-RAT offers 4 functions:

Both Queller and Goodnight (QG) and Lynch and Ritland (LR) estimators are available for relatedness calculations. For QG estimates, both symmetric and asymmetric relatedness matrices are available.

Analysis Tool

Step 1 - Enter your data (Input data format)

Step 2 - Select the appropriate analysis (Analysis descriptions)
Step 3 - Set the analysis options (Analysis option descriptions)
Method Bias Correction Standard Error Estimation
Queller and Goodnight Relatedness Omit X Individual Jackknife over Loci
Lynch and Ritland Estimator Omit X and Y Individuals Jackknife over Group
Pairwise Relatedness Omit X Group Number of Simulations
Symmetric Omit X and Y Groups
Asymmetric No Bias Correction
Output Format
Full Matrix
Half Matrix
Step 4 - Begin analysis
Processing Status