`P = e`^{Qt}

for

*any*t, by getting eigenvalues and eigenectors, using both R and Python. That's outstanding.

If you look carefully, you might notice something. There are just two terms in Q for the JC69 model:

`-0.01 (on diagonal) and 0.003333 (off diagonal)`

P has only two terms as well and they turn out to be (for t = 0.1):

`0.999 and 0.000333`

That is, the off-diagonal terms are apparently just multiplied by t, and naturally the diagonal is 1 - 3 times the other term. There was really no need for all the exponentiation of matrices, etc.

How does this happen? The formulas for the two terms in JC69 are:

But going back to the infinite series expansion for e (or just remembering the approximation for small x):

So the exponential is just

`1 - 4λt`

and we obtain:Let's take another look at the formulas for these terms in the TN93 model. Look at only the first row of P. We first consider the two exponential terms:

Approximating for small t:

Look what happens to

`P`_{13}

and `P`_{14}

:This is t times

`Q`_{13}

. Exactly the same thing happens for `P`_{14}

. `P`_{12}

is a bit more complicated, but it's just algebra:The second term is:

The third term is:

We can see that (considering both the second and the third term) there are two copies of:

`(π`_{C}π_{R}/π_{Y})βt

with opposite sign, leaving:The last term is t times

`Q`_{12}

. So I'm betting that the rest will go away. We have:but

so

How about that!

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