Question: Is there any way to quantify differences between neighbour-joining phylogenetic trees?
gravatar for matt.ward93
5.7 years ago by
United Kingdom
matt.ward930 wrote:

I am working on a project and I am currently only using the SNP data to make my trees. I would like to compare the trees made using SNP data to the trees made using indel data to ensure they are similar, however I am unsure as to how to go about doing this?

ADD COMMENTlink modified 5.7 years ago by Brice Sarver3.5k • written 5.7 years ago by matt.ward930
gravatar for Brice Sarver
5.7 years ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

There are many established ways to quantify differences between and among trees.

Perhaps the simplest is the Robinson-Foulds distance, which looks for groups present in one tree that are not present in another. The Kuhner-Felsenstein difference can also quantify differences taking branch lengths into account.

If you want a simple metric, you can look for differences among trees based on the number of nearest-neighbor interchanges (NNI), subtree pruning and regrafting (SPR), or tree bisection and reconnection (TBR) distances between them.

These metrics are relatively simple to calculate and are implemented in many R libraries and phylogenetic packages.

A word of caution: be careful making trees using model-based approaches from SNPs. There aren't any sophisticated models of evolution for SNP data, and a dataset constructed just of SNPs violates many of the assumptions of the methodologies.

ADD COMMENTlink written 5.7 years ago by Brice Sarver3.5k
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