Hi @ihoxie, glad you are using the pre-made ghost tree, but it sounds like it’s not working well for you for some reason. n=3430 is not good! It could be because you’re using a tree that doesn’t match the names in your table.
So to clarify there is some confusion with the terms (no fault of yours). There is the ghost-tree software tool (italicized) and there are also ghost trees that are just the .nwk trees that are the output of running the ghost-tree tool. Basically we just call them ghost trees because they’re not a true phylogenetic tree… it’s a hybrid of two databases.
There is an accession file included in each ghost tree folder that you can use to filter your table to match the ghost-tree.nwk files. These are the most recent trees I have made and each folder contains the file you can use, although I see now that there is a 2018 UNITE version now. I can make these in a few weeks. Where did you find a 2019 UNITE version? Either way, you need to make sure the IDs in your tables will exactly match the IDs in the ghost tree .nwk file. If you want a custom ghost tree, you would have to install the ghost-tree plugin and build a new one.
You cannot use the output from the taxonomy classifier because ghost-tree requires an OTU map. This is something I need to look into at a later time. ghost-tree was developed in 2014-2015 and published in 2016 when there was always an OTU map. So for now, ghost-tree just needs one. However, if you are using the pre-built trees to run your diversity analysis, you should not need to install and run the “ghost-tree” software tool. You just need a phylogenetic tree (a prebuilt ghost tree .nwk) to run your diversity analysis. If you are following the ghost-tree community tutorial, make sure you’re not mixing up method 1 with method 2.
The link Matthew provided will help you filter your table to keep only sequences that are in the ghost tree so you can run your diversity analysis.
Let me know if you have any more questions. Responses may be delayed due to travel. -Jennifer