Hello Everyone,
I am doing maximum likelihood trees for a set of sequences using the ITS rDNA gene and actin gene in a lichenised green alga. I understand bootstrapping, but I am not sure what the output from MEGA6 means. I get a LogLikelihood value, Ts/Tv value, and sbl value. Some questions I had:
1) How does one interpret these values?
2) What do they mean (ie. what is sbl)?
3) If one tree produces a Ts/Tv ratio of 0.7173, a sbl value of 0.72047016, and a log likelihood value of -3433.71 and another tree produces a Ts/Tv ratio of 0.6647, a sbl value of 0.27028389, and a log likelihood value of -977.59, which is the better model and why?
I appreciate any help and assistance that you can provide. I am very new to phylogenetics and so any advice is great.
Thanks!
Hi jennifer
* The maximum likelihood method uses standard statistical techniques to assign probabilities to the set of all possible phylogenetic trees for a given group of input sequences. The method requires a substitution model to assess the probability of particular mutations; roughly, a tree that requires more mutations at interior nodes to explain the observed phylogeny will be assessed as having a lower probability. This is broadly similar to the maximum-parsimony method with varying rates of evolution across both lineages and sites.
The log-likelihood is the expression to determine optimal values of the estimated coefficients. Because you want to maximize the log-likelihood, the higher value is better. For example, a log-likelihood value of -977.53 is better than -3433.71.
* ts/tv is going to differ from species to species, and even among populations and individuals in the same species. For example, for whole human genome, a ts/tv of around 2-2.1 is generally correct. But, different specific genetic regions can display different ts/tv ratios. Looking at human exomes, it appears that the ratio increases to a ts/tv of 2.8-3.0 or higher. It is therefore important to estimate accuracy another way prior to using ts/tv (for example, by SNP chip or genotyping comparison), then tweak your variant calling parameters for the highest accuracy and determine what the optimal ts/tv of your genome/exome/genetic region is. You can then use that optimal ts/tv ratio as your metric to aim for.
Ts/Tv value is the ratio of transitions (when purine substituted by another purine; or pyrimidine substituted by another pyrimidine) to transversions (when purine substituted by pyrimidine and vice versa).
LogLikelihood value is the logarithm of the likelihood function.
sbl value is the amount of Shared Branch Length
Hi jennifer
* The maximum likelihood method uses standard statistical techniques to assign probabilities to the set of all possible phylogenetic trees for a given group of input sequences. The method requires a substitution model to assess the probability of particular mutations; roughly, a tree that requires more mutations at interior nodes to explain the observed phylogeny will be assessed as having a lower probability. This is broadly similar to the maximum-parsimony method with varying rates of evolution across both lineages and sites.
The log-likelihood is the expression to determine optimal values of the estimated coefficients. Because you want to maximize the log-likelihood, the higher value is better. For example, a log-likelihood value of -977.53 is better than -3433.71.
* ts/tv is going to differ from species to species, and even among populations and individuals in the same species. For example, for whole human genome, a ts/tv of around 2-2.1 is generally correct. But, different specific genetic regions can display different ts/tv ratios. Looking at human exomes, it appears that the ratio increases to a ts/tv of 2.8-3.0 or higher. It is therefore important to estimate accuracy another way prior to using ts/tv (for example, by SNP chip or genotyping comparison), then tweak your variant calling parameters for the highest accuracy and determine what the optimal ts/tv of your genome/exome/genetic region is. You can then use that optimal ts/tv ratio as your metric to aim for.
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