Torsten Seemann

@felipelira what is `get_homologues` ?

I wouldn't trust it. Maybe compare it to other methods like `proteinortho` and `MMseqs2`

No one seems to be able to get rid of that bug. It does not affect the outputs.

You seem to be mixing Linuxbrew, Ubuntu, and Conda. That will cause many problems.

@philippbayer I am told by @slugger70 that `libxml2` is some conda bug right now!

Roary is fast because it expects lots of _very_ similar proteins and uses `cd-hit` to speed that part up. After that it falls back to ALL vs ALL `blastp`. Metagenomes...

useful paramaters are ``` -i minimum percentage identity for blastp [95] -iv STR Change the MCL inflation value [1.5] ``` Increasing inflation will increase granularity, that is it will produce...

Roary only supports `kraken` (version 1) Where is the link to the tutorial you are doing?

Roary also uses gene synteny to cluster paralogs. See https://github.com/sanger-pathogens/Roary/issues/395

I second this suggestion. Either add a `-s` (stats?) option to report all sorts of columnar statistics, characters used etc. OR Always output this to `stderr` as part of the...