roblanf

Using a starting tree, and then each bootstrap with: ``` fasttree -nosupport -nome -nt -fastest -intree "$START_TREE" $bootpre'0.fa' > $bootpre'unrooted.tree' ``` Saves 2/3 of the time BUT, it also massively...

Good point @bqminh. In this case though, both are with fasttree. I should have made that clear. The first one is 100 bootstraps where each bootstrap alignment first comes from...

Hi @lpipes, there are two parts to this answer. First, the most recent global tree contains almost 3M sequences, although that's still fewer than in the alignment. The reason for...

Huh, that's odd. I would have done the same, like: tar -xf alignment.tar.xz I'll have to take a look next week. But you could try doing the xz first, like:...

Hi @qingzhao0512, sorry - I have no idea quite how to fix this, or even quite what you mean? What platform are you using?

Nice idea. I'll keep it on the list for now. It would neaten the code for sure.

Thanks for checking up on that Angie. The trees are about to move to GISAID and be hosted / computed there, so very soon will be a great time for...

@hforoughmand if you can let me know what you're trying to do, I can try to give you some advice. In it's current version the repo is set up to...

For 10K samples, assuming lots aren’t already in an existing tree, I think the best approach would be: 1. Align as in the current repo (code should work fine) 2....

If you have samples after the initial 10K, then this repo should work fine. One thing you should consider is using UShER to place samples instead of IQ-TREE. Both work...