Question: Raxml/Gubbins Max Likelihood Tree branch units problem
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gravatar for earlsm
4 months ago by
earlsm0
earlsm0 wrote:

Hi there,

I put about 200 staph aureus isolates through snippy and core snippy to get a full multiple sequence alignment. I then put the MSA through Gubbins (specifying an outgroup and using the raxml_model GTRGAMMA) in order to make a tree which removed SNPs potentially associated with recombination. I then loaded the tree file onto iTree of Life (iToL) and found that its topology was as expected.

However, when I looked at the branch labels, they ranged from about 1.0435 to 269.536072. As I made a MLT, I was expecting the branch units to be in "substitutions per site" and so be very small numbers. It's as if I have made a distance-based tree and the branch units are in SNPs.

Does anyone know what has happened here and how I can get the branch units to "substitutions per site"? I am new to bioinformatics so it could be something very simple. Would really appreciate any help I can get!

Thanks,

Megan

snp phylogenetics genome • 105 views
ADD COMMENTlink written 4 months ago by earlsm0
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