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.

Andrii and Gael,

Thank you so much for your explanations. They help me greatly!