Sergei Pond

Dear @gwct, The `--rooted` option works with an example 3-taxon file for me (see attached). Keep in mind that the relative lengths of the two branches coming off the "root"...

Dear @gwct, Thanks for this detailed report! I can confirm the inconsistency and will track it down. I'll post a note here once a fix is available. Best, Sergei

Dear @rsiani, You should be able to run BUSTED-PH on ~1,500 sequences in a reasonable amount of time (~1 day or so, would be my guess). How long is your...

Dear @gwct, OK, so the issue is with the `--kill-zero-lengths` option (`Yes` by default). This option exists to accelerate fitting when there are zero internal branch lengths (collapsed internal branches,...

Dear @rsiani, Generally, you get a ~3-5x performance hit with SRV on. Here it could be worse than that because of the additional memory overhead. Each **branch** will require the...

Dear @gwct, Happy to help -- great questions. Best, Sergei

Dear @liamfriar, HyPhy is not exactly *re*rooting, but rather *un*rooting the tree here. That's mostly because `tree-label.bf` is meant as preprocessor for downstream analyses in HyPhy, which (for the most...

Dear @mbarkdull, Firstly, power will generally increase for larger data sets, so a much smaller "test" group could lead to some issues. There are several considerations right off the bat....

Dear @sjellerstrand, Can you include the command you use to call `hyphy` with? One suggestion is to use absolute paths and see if that helps. Best, Sergei

Dear @kullrich, There is no option in `pre-msa.bf` to retain sequence ordering. For HyPhy, sequence ordering is immaterial. However, if you need to maintain such ordering for downstream analyses, perhaps...