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The installation instructions specify Python =>3.6,

Now you mention it, I had issues with 3.8 too, but I ended installing 3.7.10 and everything works (in case you want to try). Can't comment on the other stuff...

I'm running Infernal on fungal genomes, mostly following the Rfam recommendations, i.e. using `-Z` to calculate e-values, only using CM (`--nohmmonly`), and using the gathering threshold (`--cut_ga`, [curated thresholds](https://docs.rfam.org/en/latest/glossary.html#gathering-cutoff)). The...

I installed it last week with `mamba` without issues. I had to manually include `perl-bioperl` and `perl-local-lib` though.

Related to point 4, it would be great if there was an option to change the range of the colour gradient. If you compare close relatives it is hard to...

Hi @gamcil , my idea is to adjust the colour scale to the range of interest, i.e. the second option you mention. I'd usually be only interested in moving the...

As user, YAML would be easier to write/implement if I wanted to make my own custom pathway. Regarding the naming conventions, each "step" in the pathway modules are called "reactions",...

A very common way is using shapes/colours on the nodes. They are a common approach that many tree viewers incorporate, e.g. this https://media.nature.com/lw926/nature-assets/ismej/journal/v10/n10/images/ismej201643f2.jpg or this https://journals.plos.org/plosbiology/article/figure?id=10.1371/journal.pbio.1000602.g003 I'd also suggest to...

Related to this, I've been trying to run `colabfold_batch` from a ready `a3m` file but it still tries to connect to the `https://a3m.mmseqs.com/` server while asking for a local GPU....

@martin-steinegger that's what I thought. I generated the `a3m` through `colabfold_search.sh` and then `split_msas.py` but `colabfold_batch` still tries to connect. I know this is the case because when I run...