Creating a tree using your own tree builder
The augur tree command is a light wrapper around tree building programs such as IQ-TREE, RAxML and FastTree. It’s possible that the functionality you want isn’t available in those programs, or that it is available but that augur tree doesn’t expose the functionality you need. The solution is just to use your own tree building program directly. This guide explains the general approach you can use.
Augur tree allows you to mask certain problematic sites before tree-building via augur tree –exclude-sites <exclude_file> –alignment <alignment> , where each line in <exclude_file> is a 1-based nucleotide position to mask from the alignment. We can recreate this via the following command:
augur mask --sequences <alignment> --mask <exclude_file> --output <masked_alignment>
If you use this, remember to use the <masked_alignment> file for tree building, not the input <alignment> file!
Build your tree
This is up to you! The end result should be a newick tree file with branch lengths representing nucleotide divergence (or similar). In a typical nextstrain workflow, this file will be handed to augur refine for temporal inference (see below if you also want to skip this step). Note that augur refine may change the tree structure in two ways:
Rerooting (avoid via augur refine –keep-root)
Resolving polytomies using temporal information (avoid via augur refine –keep-polytomies)
There are some gotchas involved in tree building, such as:
IQ-TREE will change taxon names if they include any of the following characters: /|()*. This will result in the tree and alignment falling out of sync. Other tree builders may have similar behavior.
Bootstrap values are allowed, and should be parsed correctly by augur refine.
Avoiding augur refine
While augur refine is typically used to reroot the tree and infer the times of internal nodes, it also performs two important tasks which subsequent augur commands expect:
Labels internal node names. These are typically in the format NODE_0000001, but this is not required.
Stores branch lengths already present in the newick tree as a node-data JSON file, which augur export uses.
If you can address both of these then you can easily skip the augur refine step.