SNP Analysis and phylogenetics

Introduction

Phylogenies have typically be inferred from gene sequences where both variant AND invariant sites are included and this is very useful for the issue of branch length estimation.

When constructing trees from SNP analyses, what we have is an account of variant sites only.

Links

Andrew Rambaut suggestion

Is to introduce the number of invariant sites in the shape of counts for each of the four bases. His post is here.