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[igraph] Building a graph from a genetic distance matrix and finding com

From: Laura Thompson
Subject: [igraph] Building a graph from a genetic distance matrix and finding community structure
Date: Mon, 27 Jan 2014 13:20:49 -0500

Dear Igraph Users,

I am using 2 different square genetic distance matrices (26 rows and columns of animal populations) to build 2 weighted and undirected graphs.  I would like to find clusters or communities in each of the graphs and determine how they differ.  However, I have a couple of questions.

1)  A (mostly) complete graph with genetic distances between all populations (a small number of the distances are 0) clusters much differently than a graph with a reduced edge set.  Does anyone know if techniques exist to identify an optimal cutoff distance value for reducing the number of edges?

2)  There are a large number of modularity metrics in igraph.  I have experimented with both the leading.eigenvector.community and the fast.greedy.community and they seem to give fairly similar results.  Are these appropriate metrics for my particular problem?

Thanks for your help!

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