Maximum likelihood analysis of Cardamine/Amomum dataset
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1. What is the likelihood of the best tree for the Cardamine binary matrix? *
2. How many groups of individuals do you see in the Cardamine AFLP tree? *
3. Analysis of the ITS dataset: What is the difference in likelihood between the tree with highest and the smallest likelihood? *
4. Analysis of the ITS dataset: What are the differences among the ten trees? *
5. What is the difference among the best ITS and the best matK tree? *
6. Rapid bootstrap analysis of the matK dataset: What is the lowest bootstrap support value? *
7. Repeated rapid bootstrap analysis of the matK dataset: Are all the bootstrap values the same? If not, why? *
8. Standard bootstrap analysis of the matK dataset: Are the standard bootstrap values same as rapid bootstrap values? Is there any trend? *
9. Is the topology of ITS, matK and concatenated tree the same or what are the differences? (Always compare rooted trees) *
10. Compare standard and rapid bootstrap values for the concatenated dataset. *
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