Difference between revisions of "SNP Analysis and phylogenetics"
(Created page with " = Links = == Andrew Rambaut = [https://groups.google.com/forum/#!topic/beast-users/V5vRghILMfw Says] that") |
|||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | = 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. | ||
| − | = Links = | + | When constructing trees from SNP analyses, what we have is an account of variant sites only. |
| + | = Relevant Links = | ||
| − | == Andrew Rambaut = | + | == Andrew Rambaut suggestion== |
| − | [https://groups.google.com/forum/#!topic/beast-users/V5vRghILMfw | + | 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]. |
| + | |||
| + | == Seqanswers thread == | ||
| + | |||
| + | 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. | ||
| + | |||
| + | = General links = | ||
| + | |||
| + | * [https://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg.2017.36.html Human Y-chromosome variation in the genome-sequencing era] by Mark A. Jobling and Chris Tyler-Smith. | ||
| + | * [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3233099 Bakker et al.] in their paper "A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type (div-cross)" discuss using '''nucmer''' and '''show-snps''' from the MUMmer package. | ||
Latest revision as of 14:23, 4 July 2017
Contents
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.
Relevant 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.
General links
- Human Y-chromosome variation in the genome-sequencing era by Mark A. Jobling and Chris Tyler-Smith.
- Bakker et al. in their paper "A Whole-Genome Single Nucleotide Polymorphism-Based Approach To Trace and Identify Outbreaks Linked to a Common Salmonella enterica subsp. enterica Serovar Montevideo Pulsed-Field Gel Electrophoresis Type (div-cross)" discuss using nucmer and show-snps from the MUMmer package.
