search

donovan-h-parks / PhyloRank

Assign taxonomic ranks based on evolutionary divergence.
GNU General Public License v3.0
21 stars 4 forks source link

Requirements for Newick Tree #4

Closed vrbrand closed 4 years ago

vrbrand commented 6 years ago

I was wondering if you could describe the requirements for the newick tree a little more. I am trying to calculate the RED scores for a proteobacterial family. I have a tree with multiple members of this family and two outliers (one that is a member of a different class, one that is a different phylum). When I decorate the tree it only labels the family for which I have multiple representatives, regardless of whether or not I use the -m 1 flag. When I run that through outliers, I get the error:

INFO: Reading tree.
INFO: Reading taxonomy.

Rank    Taxa to Plot    Taxa for Inference
family  1   0

INFO: Identified 0 phyla.
INFO: Using 0 phyla as rootings for inferring distributions.
ERROR: Rescaling requires at least 2 valid phyla.

This makes sense since the phyla are not labelled/decorated on the tree, but I'm not sure how to do that.

Can I use this program to look at a specific proteobacterial family? How many other sequences would I need to make sure it catches (and labels) multiple phyla? Is this an error with not having sufficient representatives or is there likely something wrong with my taxonomy file?

I'd greatly appreciate any insight into this. Thanks!

donovan-h-parks commented 6 years ago

Hello,

PhyloRank assumes a domain wide tree. Our companion software, GTDB-Tk, automates taxonomic classification via the method used by GTDB: https://github.com/Ecogenomics/GtdbTk

Cheers, Donovan