Hello, I've been creating a phylogenetic tree for the bacteria within my dataset using this code within the ampliseq pipeline: ""pplace_tree": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/sbdi-gtdb-sativa.r09rs220.bac120.sprepr.brlenopt.newick", "pplace_aln": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/sbdi-gtdb-sativa.r09rs220.bac120.sprepr.alnfna", "pplace_taxonomy": "/cfs/klemming/projects/snic/naiss2023-22-1217/ampliseq_analysis/sbdi-gtdb-sativa.r09rs220.bac120.sprep.taxonomy.tsv", "pplace_model": "GTR+F+I+G4", "pplace_name": "bac120.r09rs220"" However, now I saw that the tree is unrooted. How do I root the tree? Is there a function within the pipeline to do it? Thanks and kind regards!

No, there's no function to root the tree. That's easiest to do either with a tree viewer (Dendroscope, iTOL), programmatically with R (e.g. iotree) or a program like RAxML: https://groups.google.com/g/raxml/c/of7s0iWcOiI.