Distmat from strainphlan tutorial

Hi Strainphlan developers,

I am working with the strainphlan tutorial recently [StrainPhlAn3 · biobakery/biobakery Wiki · GitHub]. I followed the tutorial to run distmat using Kimura 2-parameter distance. But I see the output has almost all the entries larger than 1. I checked the distmat on their website [EMBOSS: distmat manual ]. It’s strange that this gives a number larger than 1 because the meaning of K is “the total number of substitutions (including revertant and superimposed changes) per
site which separates the two species” [https://link.springer.com/content/pdf/10.1007/BF01731581.pdf]

I am wondering if this value given by distmat is actually K*100% as a percentage? Thank you in advance for your help!

Best wishes,

Hi @auas
Thanks for getting in touch. Using the EMBOSS distmat, the distance matrix will be expressed in terms of the number of substitutions per 100 bases or amino acids, so the distance values will range between 0 and 100.


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