Strange number of trees in the allboot.tree file

[J Ramírez]

Dear all,

I have run a bootstrap analysis with 100 replicates (and only one independent search) on Garli at Cipres, and I saw that in the allboot.tre file there are a total of 2400 trees. This doesnt make sense to me, as it is stated that there should be only one tree per bootstrap repetition.
Can someone please why is this happening?

Cheers,
Juan

[Derrick Zwickl]

Hi Juan,

That doesn't make sense to me either.  I'm not sure how they have things set up behind the scenes at Cipres.  It may be that the the bootstrap replicates were intended to be split across 24 processors, but each processor did a full 100 bootstrap replicates instead of a smaller number of replicates that could then be combined to make the 100 replicates requested.

It should be fine to use 100 (or whatever number of trees you want) from the file with 2400 trees.

If you want to know more about what caused this (or report it as a bug), then you'll need to contact Cipres.

Best,
Derrick