mihkelvaher

Quicktree also performs quite well ``` sed -i "1s/.*/$FILECOUNT/" $dashingDistanceMatrix quicktree -in m $dashingDistanceMatrix > $newick # NJ-tree, https://github.com/khowe/quicktree nw_reroot $newick > final.nwk # quick and dirty rooting, http://cegg.unige.ch/newick_utils ```

That's great! Also, can smaller sketches be compared with larger ones? For example, if I have some bacteria and human in the same database, do I need to scale up...

Hi Daniel, The pull request suggested that the option is now available on main. Unfortunately, I don't know how to use it and `-o` isn't listed in `dashing sketch -h`....

Hi! Presketching Looking at the code and the help, the flag is `--presketched` and not `--presketched-only` (name of the var in code)? Did I understand correctly that `--presketched` is meant...

Hi! Maybe it's a WIP but I noticed a commit (or two) mentioning `-W` and `--cache-sketches`. While the longer version works, the shorter outputs ``` Dashing version: v0.5-5-g5210 terminate called...

I can confirm that the `-W` works now. Is the `##Names` row intentionally removed in `v0.5-5-g5210` while querying with `-Q`?

Hi! After trying out the latest version and mulling it over in the light of the issue in the beginning, I have to disagree that this is the best approach...

Maybe it's still WIP, but with `dashing dist myfastas/* --size` `v0.4.2` outputs paths/sizes ##Names and a matrix, but with `v0.4.3-16-g4a39` instead of the matrix there's this: ``` terminate called after...

TL;DR: `-T` vs default gives different results. Using another k-mer program with the same k I found some differences that should not be there. `dashing dist fastas/* --sizes -T --use-full-khash-sets...

In practice, the zero info on the diagonal is more or less irrelevant so it can be pushed to the bottom of the TODO list. Comparing the results of different...