Frequently Asked Questions

How do I interpret ultrafast bootstrap (UFBoot) support values?

This feature (-bb option) was published in (Minh et al., 2013). One of the main conclusion, is that UFBoot support values are more unbiased: 95% support correspond roughly to the probability of 95% that a clade is true. So this has a different meaning than the normal bootstrap supports (where you start to believe in the clade if it has >80% BS support). For UFBoot, you should only start to believe in the clade if its support >= 95%. Thus, the interpretations are different and you should not compare BS% with UFBoot% directly.

Moreover, it is recommended to also perform the SH-aLRT test (Guindon et al., 2010) by adding -alrt 1000 into IQ-TREE command line. Each branch will then be assigned with SH-aLRT and UFBoot supports. One would typically start to rely on the clade if its SH-aLRT >= 80% and UFboot >= 95%.

How does IQ-TREE treat gap/missing characters?

Gaps (-) and missing characters (? or N for DNA alignments) are treated in the same way as unknown characters, which represent no information. The same treatment holds for many other ML software (e.g., RAxML, PhyML). More explicitly, for a site (column) of an alignment containing AC-AG-A (i.e. A for sequence 1, C for sequence 2, - for sequence 3, and so on), the site-likelihood of a tree T is equal to the site-likelihood of the subtree of T restricted to those sequences containing non-gap characters (ACAGA).