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Frequently Asked Questions

What is the difference between maximum likelihood and maximum parsimony?

Maximum parsimony is the technique of constructing a tree with the minimum number of character state change. In contrast, the maximum likelihood of a phylogenetic tree relies on using the maximum similarity between genetic data. The data for both analyses come from the DNA or RNA sequence data.

Why is the maximum parsimony tree not always the shortest tree?

It is because only the main distinguishing characteristics are considered in maximum parsimony. When drawing a maximum parsimonious tree, the tree is always the shortest possible tree with the minimum number of taxa. However, the reliability of a maximum parsimonious tree is very high.

How many changes are needed for a good parsimony analysis?

Parsimony analysis uses the number of character changes on trees to choose the best tree, but it does not require that exactly that many changes, and no more, produced the tree. As long as the changes that have not been accounted for are randomly distributed over the tree (a reasonable null expectation), the result should not be biased.

Does parsimony minimize the number of convergences and reversals?

This is not entirely true: parsimony minimizes the number of convergences and reversals that are assumed by the preferred tree, but this may result in a relatively large number of such homoplastic events. It would be more appropriate to say that parsimony assumes only the minimum amount of change implied by the data.

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