Subtrees from StrainPhlAn3

Hi :slight_smile:

I’m new to StrainPhlAn3 and when I read the tutorial and as well its original paper, I met some problems.

I found that in the paper you have shown the subtrees’ piecharts.

Screenshot from 2023-02-25 10-40-50
In the paper, it wrote:

Country-specific subtrees for Supplemental Figures S9–S20 are computed as the largest subtrees with at least 80% of samples coming from a single country. Subclades for Figure 5B and Supplemental Figures S21–S37 are the largest subtrees in each phylogeny with the largest intra-SNVs rate <0.1%.

I couldn’t find a command in StrainPhlAn3 that can define the subtrees. For now, I have the tree files from StrainPhlAn3 and the mutation rate file, but I don’t know how to get the sub-trees. could you please give me some suggestions? Thanks a lot.

Best Regards,

Hi @LuZhang
Unfortunately, there is not an available script to define the country-based subtrees from the strainphlan trees. The original authors of the work probably made an in-house script for this purpose.