Design choice regarding bootstrapping in MAGMA

[abhi18av]

Dear @vrennie @TimHHH @mdediegofuertes

I came across a question regarding bootstrapping in the pipeline, which we don't use as of now. Previously, we have added some comments but perhaps we should outline when and why exactly one might need to tweak the IQTREE arguments

MAGMA/default_params.config

Lines 631 to 633 in e5011cb

	//Add "-bb 10000" for ultrafast bootstraps, or "-b 1000" for boring bootstraps
	// "-allnni" can be excluded to significantly speed up, but this is less accurate for closely related samples

The final arguments with which we run IQTREE at this point are as follows

iqtree \
    -s Filtering_Test.variable.ExDR.IncComplex.fa \
    -T AUTO \
     -allnni -redo  \
    --prefix Filtering_Test.ExDR.IncComplex

I am initiating this discussion on Github itself document the design choice better.

[TimHHH]

1. -allnni ensures a very thorough search of possible phylogenies, in certain cases too thorough, if you find that IQTREE consistently finds the same phylogeny for your dataset with and without this option then you may exclude it to speed up phylogenetic inference.
2. bootstrapping is used to infer a certain level of confidence (out of 100) for each split in the phylogeny, this is done by resampling and reanalysing the fasta, this standard bootstrap can be called with the -b 500 option and the bootstrap scores are included in the phylogentic outputs. >=500 recommended, WARNING: this will slow down time to results massively.
3. fast bootstrapping uses the method described here. Fast bootstrapping is done with -bb 1000, >=1000 recommended, WARNING: this will slow down time to results. Consider including -alrt 1000 to perform the recommended SH-aLRT test

This is not something one should do if not familiar with the interpretation of bootstraps, this is not something for clinicians.

[abhi18av]

Thanks @TimHHH for the answer.

This is not something one should do if not familiar with the interpretation of bootstraps, this is not something for clinicians.

My question is specially around this phrase, perhaps the research groups who are especially focused on phylogenetic trees - they might benefit from -alrt 1000 right?

If time consumption by the IQTREE process is a concern, then perhaps we can introduce a couple of flags like --fast-phylogeny and --standard-boostrap ?

Though, users can just customise using a config file so the params thing is just an idea.

[TimHHH]

If time consumption by the IQTREE process is a concern, then perhaps we can introduce a couple of flags like --fast-phylogeny and --standard-boostrap ?

If we can give each flag a section in the default parameters file then I think this would be great. Such a section would then include the line with all commands for the given flag so that users can change the parameters. Something along these lines:

#accurate maximumlikelihood phylogeny only DEFAULT
--accurate-ml-only = '-allnni'

#fast maximumlikelihood phylogeny only
--fast-ml-only = '-fast'

#fast-bootstrapped-phylogeny
--fast-bs-phylogeny = '-bb1000 -alrt 1000'

#standard-boostrap
--standard-boostrap = '-bb1000'

maybe also reflect the used flag as part of the output prefix.

[vrennie]

Sounds good to me!

[abhi18av]

Oki doki, I've now added 4 iqtree_* specific parameters which reflect the scheme outlined earlier

1e9c702

[vrennie]

Hi @abhi18av can you inform me where I need do add the --standard-boostrap = '-bb1000' if I am launching on Nextflow? I tried it here but I don't think it worked:

https://tower.nf/orgs/TORCH/workspaces/XBS-Nextflow/watch/v6E4UB2ccO5Qt

[abhi18av]

Hey @vrennie the new parameters are added as

1. On CLI --iqtree_standard_bootstrap, you need to use the flag
2. In the params file, you need to use iqtree_standard_bootstrap: true

Please check here for other options #164 (reply in thread)

[TimHHH]

The bootstraps can be found inside the *.treefile .

Figtree will say that it has identified some undefined label, you can give it the name ‘bootstrap’ or whatever you like.

The bootstrap labels can then be visualised by enabling node labels and specifying that the ‘bootstrap’ has to be displayed there.