Frequently Asked Questions

Table of Contents

• How do I interpret ultrafast bootstrap (UFBoot) support values?
• How does IQ-TREE treat gap/missing characters?
• Can I mix DNA and protein data in a partitioned analysis?

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).

Can I mix DNA and protein data in a partitioned analysis?

Yes, you can! In fact, you can mix any data types supported in IQ-TREE, including also codon, binary, morphological data. To do so, each partition should be in a separate alignment file. Then, prepare a NEXUS partition file which may look like:

#nexus
begin sets;
    charset part1=dna.phy: *;
    charset part2=protein.phy: *;
    charpartition mymodel=GTR+G: part1, LG+I+G: part2;
end;

Here, it is assumed that dna.phy and protein.phy are DNA and protein alignment files, respectively. IQ-TREE will automatically detect the sequence types, which works correctly in 99% of the cases. If you want to explicitly specify the sequence type, the partition file may look like:

#nexus
begin sets;
    charset part1=dna.phy:DNA, *;
    charset part2=protein.phy:AA, *;
    charset part3=dna2.phy:CODON, *;
    charpartition mymodel=GTR+G: part1, LG+I+G: part2, GY:part3;
end;

The advantage is that you can specify a codon partition (see above), which would not be possible in the first example because part3 will be detected as a DNA partition.

Finally, please note that you can also specify the site ranges within each alignment. For example:

#nexus
begin sets;
    charset part1=dna.phy:DNA, 1-150;
    charset part2=protein.phy:AA, 1-100 201-300;
    charset part3=protein.phy:AA, 101-200;
    charpartition mymodel=GTR+G: part1, LG+I+G: part2, WAG+I: part3;
end;