Rhett M. Rautsaw

pxnj and pxupgma tree inference

6

Running a neighbor joining tree on the same alignment in Geneious vs. phyx results in completely different trees. The tree in Geneious makes sense....the tree from pxnj is completely unexpected....

Is there a way to have ggparagraph format text within the paragraph differently? Like if a scientific name in the paragraph needed to be italicized or you wanted to add...

freqQuad empty

1

**Describe the bug & to reproduce** When running `-t 16` or `-t 32`, ASTRAL appears to complete but `freqQuad.csv` is completely empty. The only error reported is: ``` Final quartet...

With ASTRAL you can provide a mapping file with `-a`. Is there any way to incorporate a mapping file with DiscoVista if the tips in your gene tree do not...

Log scale

4

Is there a way to log scale a geom_fruit facet without simultaneously log scaling the underlying phylogeny?

Open Terminal instead opens a text document

1

### Describe the bug When I select to open a terminal on any of my Orbstack Rocky machines, it instead opens a text document in VSCode ``` #!/bin/sh -e cleanup()...

sourmash tax metagenome krona and kreports are vastly different?

2

I am running sourmash v4.8.14 on a PacBio HiFi long read dataset. It is a test dataset with ~50% representation from two cultured taxa. I am using this snakemake workflow...

Hi Dr. Cheng, First, thanks for making such a great software! I use it or help answer questions about it almost every day. This is less of an issue and...