Phylogenetic tree tools

[colinbrislawn (Colin J Brislawn)]

@Antani

What I would like to do is to obtain a phylogenetic tree after the taxonomic classification, in order to display the annotation of my classified features.

Do you have any suggestions for this?

Kind of. But not really.

When you have ITS reads, it's had to build a reliable tree for the reasons outlined here:

Analysing fungal ITS data - questions about the pipeline - phylogenetic analysis

Hi @Cat , This is sort of true — ITS alignments are sometimes used for examining phylogeny of closely related fungal species. Thus, fungal taxonomy papers (which are generally concerned with parsing closely related species/groups) will sometimes use this for comparison of isolated strains. Indeed it is. In a mycobiome study you are almost inevitably comparing fungi from highly divergent groups. ITS will not generate a reliable alignment/phylogeny for such divergent groups. As a non-coding r…

So you can push your ITS reads through a MSA -> treebuilding pipeline, but the results will be trash highly stochastic and unreliable.

What sort of figure do you want to make with the tree? Perhaps there is another way to get there, and we can plan for that.