To be fair I should report my incorrect and somewhat angry response to the rejection of the appeal

Really I give in.

I will do fasttree using seqboot for bootsrap but this is from the manual

“00 fast-global bootstraps took just 20 hours, and the resulting support values were strongly correlated with the traditional bootstrap (r=0.975).”

So it is NOT comparable to the bootstrap it just correlates to the bootstrap. So again the “expert” is actually unaware of how it works.

Both trees are created with ML methods using a GTR+G evolutionary model – using different implementations sure. I can do both in fasttree but it would show what exactly?

The figures are illegible – you could try zooming as they are vector images but that asks too much of a someone with a PhD

There is one reference missing to my own work.

As they say “ whatever”.

This is going to give me a two for as I will resubmit it next week with everything done and a new title and excluding both of those editors.

Thanks

Andy

On this I am definitely wrong. You can bootstrap normally using seqboot and consense. This correlation is only true if you specify an initial tree.

However, there are over 1000 variable sites. For the ideal (non-parametric) bootstrap estimate you need nCr (2n-1,n) permutations = 10 x E 600 calculations (Efron and Tibshirani). Sampling even 1000 bootstraps is insignificant. For 100 sites it is 5 x E 59. It is likely that bootstrap estimates are far from convergent, but that would need testing for each tree by increasing the bootstrap number until the percentages remain fixed.