Is there a way to incorporate Ultrafast bootstrap in the pipeline?

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I wanna use the nextstrain pipeline for describing novel pangolin sublineages within a specific lineage.
Is there a way to incorporate ultrafast bootstrap in the pipeline?
Should I just modify the line “tree-builder-args” of parameters.yaml?

2

Hi @fhsantanna, yes, you can specify most IQ-TREE parameters like you through the --tree-builder-args argument of augur tree. Some IQ-TREE parameters are hardcoded in augur tree, though, so you may get an error if you try to override those default parameters. Here is an example of how augur tree runs IQ-TREE for the Zika tutorial.

iqtree -ninit 2 -n 2 -me 0.05 -nt 1 -s results/aligned-delim.fasta -m GTR
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In fact, I got an error.

ERROR: Shell exited 2 when running: iqtree -ninit 2 -n 2 -me 0.05 -nt 8 -s results/novel_vinte_oito/aligned-delim.fasta -m GTR -B 1000 > results/novel_vinte_oito/aligned-delim.iqtree.log
Command output was:
Ultrafast bootstrap does not work with -fast, -te or -n option

4

Darn, I’m sorry that didn’t work out! The best next step would be to replace augur tree in your workflow with a direct call to iqtree and the parameters you’d like to use. Since augur’s tree command is mostly a light wrapper around each tree builder anyway, you might be able to get away with dropping in the iqtree command directly. Worst case, you may need to add some equivalent pre- and post-processing steps to your workflow to replicate what augur does.

In the longer term, we’ll need to discuss as a team about a better way to enable overriding the default arguments with the --tree-builder-args command. This is something we’ve discussed before for the augur align step, too.

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5

Thanks. It’s ok. As you recommended, I built a tree using iqtree directly.

6

Dear @jlhudd ,
How to infer the confidence of clades in the nextstrain tree? There is already some way to generate a tree with the nextstrain containing the boostrap values? If not which output can I use in iqtree?
I didn’t find the align-delim.fasta output in my nextstrain results. My nextstrain result did not generate this file no directory results. Although I got the final results in the auspice directory, with success.
The files with the closest names are:
aligned-delim.fasta.log, aligned.fasta.
I would like to build a tree in nextstrain or iqtree containing the clades names (alpha, beta, gamma, etc), time and bootstrap.
That’s why I asked about the aligned-delim.fasta file, I believe I need this one to generate a booststrap tree.
Thanks for your attention,
Best,
Leandro