pvanheus

I see Steve (@biologyguy) added an extra hour to the schedule. That's wise, if you can do it. I taught the gapminder lesson at PyConZA recently and ran out of...

I think the documentation hasn't kept up with the changes in the code because I find the same problem. When I look at older code on github I see the...

What I mean is one input, but multiple replace operations. So e.g. input: ``` ABC DEF 99% pure Galaxy ``` replace operation one: ABC -> abc replace operation two: 99%...

@joblingm - can you make a Galaxy history with this error and link it to this issue?

Following on from this, the [logic](https://github.com/Cibiv/IQ-TREE/blob/master/tree/phylotree.cpp#L4889) for collapsing identical sequences means that if there are N identical sequences, N-1 are collapsed into a single entity (with branch length 0 between...

btw to address the zero branch length issue I noted above (an independent question from the shape of the tree), [`insertTaxa()`](https://github.com/Cibiv/IQ-TREE/blob/master/tree/mtree.cpp#L2347) could be altered to use `min_branch_length` rather than `0.0`....

interesting - I think this issue has some overlap with https://github.com/Cibiv/IQ-TREE/issues/163

This is [this tool](https://github.com/oschwengers/referenceseeker) and indeed it looks good. It will need a data manager (DM) as well as a tool. A similar tool is [refseq_masher](https://github.com/phac-nml/refseq_masher) which has been added...

Hi @pimarin - yes, I don't think refseq_masher has an option for updating its database. As to a data manager: this is a special kind of tool that updates a...

I made a very small start on this: ```xml 0.1.10 clair3 History Built-in ```