Time scale of the inferred rate matrix Q

[perryXuu]

Hi everyone,

I'm trying to understand the substitution rate matrix inferred (in the .iqtree file).

Rate matrix Q:

A -1.248 0.3763 0.6966 0.1752
C 0.1777 -0.8777 0.3713 0.3287
G 0.3334 0.3763 -0.8849 0.1752
T 0.1777 0.7059 0.3713 -1.255
The date I provided is in YYYY-MM-DD format, and I wonder what is the time scale for this rate matrix. Is it in Year automatically? Didn't find this information in the documentation, I would be really appreciating any help!! Thank you!!

Best,
Perry

[roblanf]

The rate matrix does not have units or a timescale. These are relative values, also known as instantaneous rates.

You can convert these into probabilities of change along a branch of length t by exponentiating this matrix. The RevBayes documentation is quite good on this (and there are videos too, though I haven't watched them!):

https://revbayes.github.io/tutorials/ctmc/

As a side note (but an important one in this context) please note that in IQ-TREE, molecular dating is done by a separate program, LSD2, which is run after IQ-TREE finishes. LSD2 relies on the branch lengths and time constraints you supply. Thus, IQ-TREE itself does not do anything with your date information when calculating the Q matrix. Indeed, IQ-TREE is completely ignorant of any notion of absolute time.

[perryXuu]

Thank you so much! That was very helpful!!