Negative Log likelihood value for gene tree using MEGA
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6.0 years ago
Elizabeth ▴ 30

Hi all, I have constructed a gene tree using 27 genes using the Maximum likelihood method with MEGA X. However, even though the bootstrap values on the branches look good, the likelihood value given by MEGA for that tree is -9745.782. I don't understand. Please help.

MEGA negative likelihood • 3.9k views
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Yes it does help a bit. Based on that link, I gather that it is commonplace to have negative log likelihood values for phylogenetic trees?

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6.0 years ago
h.mon 35k

I will copy / paste directly from Wikipedia:

For many applications, the natural logarithm of the likelihood function, called the log-likelihood, is more convenient to work with. This is because we are generally interested in where the likelihood reaches its maximum value: the logarithm is a strictly increasing function, so the logarithm of a function achieves its maximum value at the same points as the function itself, and hence the log-likelihood can be used in place of the likelihood in maximum likelihood estimation and related techniques. Finding the maximum of a function often involves taking the derivative of a function and solving for the parameter being maximized, and this is often easier when the function being maximized is a log-likelihood rather than the original likelihood function, because the probability of the conjunction of several independent variables is the product of probabilities of the variables and solving an additive equation is usually easier than a multiplicative one.

As a by product of likelihoods values being really tiny (close to zero), log-likelihood values are negative.

Absolute likelihood values do not say if the recovered tree is good or not, but, when estimating trees with the same dataset using different substitution models, likelihood values can help choosing the best tree.