Where is strainphlan_ggtree.R and strainphlan_ordination.R

Microbial community profiling StrainPhlAn
1

Hi,
I am going through the StrainPhlAn 3 tutorial, and want to run these commands:

strainphlan_ggtree.R RAxML_bestTree.s__Eubacterium_rectale.StrainPhlAn3.tre ../metadata.txt s__Eubacterium_rectale.StrainPhlAn3_concatenated.aln strainphlan_tree_1.png strainphlan_tree_2.png

strainphlan_ordination.R strainphlan3_concatenated.distmat ../metadata.txt strainphlan_ordination.png

However, the R scripts strainphlan_ggtree.R and strainphlan_ordination.R does not seem to exist.

Please, how can I resolve this.?

1 Like
2

Hi @paulokoroc,
You could find these scripts in the BreadCrumbs repo: https://github.com/biobakery/breadcrumbs/tree/master/breadcrumbs/scripts

Best,
Aitor

3

Thank you very much!