jo

Hi @iaunicorn, so far we have support for bacteria and recently also archaea. I would say it depends on your demands, if you are just interested in the metabolic capacities...

Do you mind opening the new issue for the blast problem? then this one can remain for the other species/fungi related question :) (and please post the output of `./gapseq...

Hi @cdiener thanks for pointing this out! We hope to have a conda package available soon! Right now, I added some hints to the [readme](https://github.com/jotech/gapseq/blob/master/docs/install.md) how to install all needed...

good idea thanks! we try to come up with some alternative installation in the near future :)

just as intermediate solution, we added a [conda installation tutorial](https://github.com/jotech/gapseq/blob/master/docs/install.md#conda)

Hi Edoardo, I had a look at your example, it's an interesting case! The problem is a bit related to the methanogenesis itself that operates at the thermodynamic limit of...

just as a side note: Acetobacterium woodii is not at all a methanogen! This could also contribute to the fact, that methanogenic genes are not infered and gap filling to...

just to add to add shortly: candidate carbon sources and fermentation products are listed in: https://github.com/jotech/gapseq/blob/master/dat/subex.tbl

Hi @Erique29 do you mind to share which carbon sources are missing? Maybe we can add them so that they could be found by default

hi, yes you can load xml files in R using the package sybilSBML ```R library(sybilSBML) mod