Branch lengths in exported tree files

User Questions
1

Hello,

I have been working with diamond and megan6 on a large metagenomics dataset and am now interested in performing some analyses outside of MEGAN. I was able to export otu tables, biom files, and tree files, but some analyses (such as unifrac) require the branch lengths in the tree files. However, I cannot find the lengths in the exported files or in the default ncbi.tre. I have taken a look at the ncbi data dumps, iTOL, and a few other places but no success. Any advice? Do I compute them myself?
Sorry if this is a simple or silly question, I am new to this.

2

There are no branch lengths in the NCBI taxonomy because it is a hierarchical clustering system based on taxonomic ranks, not an evolutionary tree. You could assign each branch the length one, in which case the distance between e.g. two species would be (twice) the number of taxonomic ranks that the differ by, e.g. distance
2 would mean “differ at the genus level”, or by one rank.
Hope that helps

3

Thanks Daniel. I had a misunderstanding about the nci taxonomy.