Relatedness Calculator

Current version: 1.0

Developer

Nolan Lawson

License

WTFPL, but attribution would be nice.

Summary

Java library for calculating the genetic relatedness between two individuals, e.g. brother-sister (0.5), parent-child (0.5), grandparent-grandchild (0.25), cousin-cousin (0.125), or even more exotic relations like "dad's second cousin" (0.015625).

Parses common English phrases. Draws Graphviz graphs. Calculates both the degree of relatedness and the relatedness coefficient, as described in this Wikipedia page.

Inspired by a dude on a message board wondering if it was cool for him to be dating his dad's second cousin. (Answer: it's probably okay.)

Demo

A live version of the Grails frontend app is available to demonstrate the functionality.

Download

Get the latest JAR here.

Usage

Calculate the relatedness coefficient between a brother and sister:

RelatednessCalculator.calculate(BasicRelation.Sibling).getCoefficient(); // returns 0.5

Calculate the degree of relation instead:

RelatednessCalculator.calculate(BasicRelation.Sibling).getAverageDegree(); // returns 2.0

Calculate the relatedness coefficient for a more complex relation, if you know the common ancestor(s):

// overhead on a message board: "her dad is my grandma's cousin"
// i.e. they share two ancestors - his 2 great-great-grandparents are her 2 great-grandparents
Relation relation = new Relation(new CommonAncestor(4, 3), new CommonAncestor(4, 3));

RelatednessCalculator.calculate(relation).getCoefficient(); // returns 0.015625

Calculate the same relation using plain English:

RelatednessCalculator.calculate(RelativeNameParser.parse(
        "grandma's cousin's daughter").getRelation()).getCoefficient(); // returns 0.015625
        
RelatednessCalculator.calculate(RelativeNameParser.parse(
        "dad's second cousin").getRelation()).getCoefficient(); //returns 0.015625

Draw a pretty graph for Graphviz:

// returns a Graphviz graph that looks exactly like the picture in this README above
RelativeNameParser.parse("double cousin", true).getGraph().drawGraph();

You can also see the unit tests for other ideas about how to use the code.

Frontend code

This code is a Java backend to the Relatedness Calculator Interface Grails app.

Maven usage

Download the code, build, and install it:

git clone https://github.com/nolanlawson/RelatednessCalculator
cd RelatednessCalculator
mvn install

Then just add the following dependency to your pom.xml:

<dependencies>
  ...
  <dependency>
    <groupId>com.nolanlawson.relatedness</groupId>
  	<artifactId>relatedness-calculator</artifactId>
  	<version>1.0</version>
  </dependency>
  ...
</dependencies>

Credits

Thanks to Richard Dawkins for his easy-to-understand explanation of how to calculate relatedness in The Selfish Gene.