Combining different approaches.#
When the phylogenetic inference is the core of your study, it is highly recommended to replicate the phylogenetic tree with different approaches. This is most commonly achieved by combining the support from different trees obtained by independent runs of maximum likelihood and Bayesian approaches. Although not always it is possible to apply different approaches to the same dataset, for example for very large datasets a bayesian inference might fail to converge; or when estimating molecular ages a bayesian approach is much better suited since it allows uncertainty in the priors. Other options could be to:
(i) use different softwares (RAxML-ng vs. IQ-TREE),
(ii) apply different models of evolution (GTR vs. CAT),
(iii) or even to replicate the alignment with different softwares, options or reversing the sequences before aligning.