roblanf

That's a good question. I only keep the identical sequences in IQ-TREE, because the code in for removing them in IQ-TREE is not well optimised. I don't keep them in...

Hi! IQ-TREE dev (well, kinda, I sort of help a bit) here. This looks like an IQ-TREE issue not an issue with snp-sites. Can I suggest you post this issue...

Here's my suggestion for what would seem natural from a users perspective. A single `--update` command which just adds to `-t` (starting tree) as follows: `iqtree -s aln.fa -t start.tree...

We had a meeting about this yesterday, so I wanted to take some notes here. Given an input tree that could have multifurcations, and an alignment that has all of...

Another point from another meeting. James has a strong intuition that if we add too many new sequences at once, we'll make life difficult for ourselves. Specifically, he thought that...

One option in IQ-TREE (since it's not built for SPR or TBR moves) would be addition via MP (already implemented) followed by local NNI moves that follow each sequence around...

A question - @minh and @JamesBarbetti, how long do you think it would take to implement each of these steps: 1. Local NNI moves for added sequences 2. An ML...

Oops. Sorry, I would have been more polite if I'd realised I didn't have privileges to assign this to myself!!! Anyway, I'll take care of it.

maybe need to specify bootstrap replicates with `-b`?

confirmed: use `-b 100 --tbe` or some higher number of course