The bioBakery help forum

Understanding branch length from strainphlan output

Hi @aitor.blancomiguez ,

Once again, thanks for developing this tool. New to strainphlan. How should I interpret the branch length from the resulting strain phylogeny tree generated? Would it be correct to say that the longer the branch length between two strain’s on the unrooted tree the more different their concatenated marker sequences are?

Do you recommend any resource for understanding RAxML tree?

Best,
JC

Hi @Jeffrey_Chiu
Your are right, the longer the branch length between two strains, the more different the strains are. If you are interested in ways to visualize your data for interpretation, in our tutorial we proposed several options: StrainPhlAn3 · biobakery/biobakery Wiki · GitHub
If you are interested on identify similar strains, you can take a look on this thread: Strain Identity Cutoff - #5 by aitor.blancomiguez

Best,
Aitor

Hi @aitor.blancomiguez,

Thanks for the pointers. Do you have information on how the branch lengths are calculated? For example: something like 0.1 length would be 0.1 bp difference/site?

Best,
JC

Hi @Jeffrey_Chiu
I think this post will be useful for your questions:
https://groups.google.com/g/raxml/c/Vq8nAENhvx8

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