Closed xvazquezc closed 3 years ago
Hi. The RED value calculated by PhyloRank is the median value of all valid phyla rootings. It appears your tree does not define any phyla. As such, it will only proceed if you indicate the --fxied_root
flag which indicates it should calculate RED using the rooting as it exists in your provided tree.
There are actually 9 phyla in the tree, but they only have a single class each. I guess that would be the issue.
As such, it will only proceed if you indicate the
--fxied_root
flag which indicates it should calculate RED using the rooting as it exists in your provided tree.
Would there be any fundamental difference compared to not using the --fixed_root
flag aside of that? I mean in terms of e.g. interpretation and/or reliability of the values in the output
Assuming you trust the rooting of your tree, using a fixed root is preferable. The challenge with the GTDB is that there isn't an accepted rooting for the bacterial tree so we make the pragmatic decision to take the medium value over plausible rootings.
Hi there, Does the
TRUSTED_TAXA_FILE
have any specific formatting requirements? I've been trying to use that option but I'm not able to make that option work. Contents seem to be always ignored (trusted.txt
is a list of phyla). I get something like this:I seem only able to make it run if I use the
--fixed_root
option. This is not a whole-domain tree but a section of it