Difference between revisions of "SNP Analysis and phylogenetics"
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Is to introduce the number of invariant sites in the shape of counts for each of the four bases. His post is [https://groups.google.com/forum/#!topic/beast-users/V5vRghILMfw here]. | Is to introduce the number of invariant sites in the shape of counts for each of the four bases. His post is [https://groups.google.com/forum/#!topic/beast-users/V5vRghILMfw here]. | ||
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| + | == Seqanswers thread == | ||
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| + | Where [http://seqanswers.com/forums/archive/index.php/t-18556.html it] mentions that the tree topology will probably be coorect, but that the branch lengths may be unreliable and most likely on the long side. | ||
Revision as of 13:47, 4 July 2017
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.
Seqanswers thread
Where it mentions that the tree topology will probably be coorect, but that the branch lengths may be unreliable and most likely on the long side.
