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I was reading about bootstrap in phylogenetics and it got me wondering that amongst all of the methods (UPGMA, Maximum Likelihood, Parsimony, Neighbour joining method) which method generally provides the largest bootstrap support? Or does that vary from problem to problem?

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For sequence data, UPGMA is not really accepted anymore. Maximum parsimony and Neighbour-joining are usually used because they are quite fast and they give you a relatively good idea about the phylogeny.

You should not decide based on which method gives you the highest bootstrap.

For publication, it is recommended to use either Bayesian consensus tree (MrBayes is popular program) or a maximum likelihood tree (RAxML or MEGA are popular for ML). For maximum likelihood bootstrap (BS) is used and the confidence is relatively high if at least reaches 80 (%). For Bayesian, instead of bootstrap Bayesian posterior probability (BPP) is used. For BPP it has to be at least 0.95 to be significant.

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  • $\begingroup$ Any sources you could add? $\endgroup$
    – AliceD
    Jan 20 '17 at 11:01

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