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What is the best bootstrap replicates I can use?

If I have a couple of (viral) multiple sequences alignments with 200 to 400 nucleotides long, can I use bootstrap replicates of 100 or 300 or 500 instead of 1000? Please, what are the advantages/disadvantages for using less than 1000?

sequence bootstrap phylogenetic tree
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written by a.alsayed.phd • a.alsayed.phd

I think it is very unclear what you are asking. Technically you "can" do a lot of stuff, like shooting yourself in the foot, running 1000 bootstrap replicates on a large sample, etc. but it depends on context. Please don't be afraid of trying things out, and explain what you are doing exactly.

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written by Michael Dondrup Michael Dondrup

My understanding is that bootstraps theoretically 'throw out' a column of the alignment, redraw the trees, and calculate the number of times a given split occurs. It would probably not make sense then to do more bootstraps than you have alignment columns, since it'd start to be redudant (someone correct me if I'm totally wrong).

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written by Joe Joe

Generally, what are factors determine the bootstrap replicates number that I have to us? can I use 100 or 200 instead of 1000? I have alignments of short seguences length (i.e 200 to 400) from Sanger sequencing of viral-samples

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written by a.alsayed.phd • a.alsayed.phd

Don't add comments as answers.

There are no determining factors as such, you really just need to do as many as you have the computational resources and time to do. It depends on your input data - if your alignment is trash, no amount of bootstrapping will save it.

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written by Joe Joe

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