Andrzej Zielezinski

@shadowFAQs I recall that class names weren't underlined. Also, the formatting in the example from this repo indicates a preference for clear formatting.

Thank you for the update. Everything's working smoothly now.

Hi, I'm sorry for the inconvenience. I wrote alfpy primarily for educational purposes and small datasets, so it doesn't perform well with large-scale data and long _k_-mers in protein sequences....

Hi, thanks for your feedback and for using Vclust! You are correct - currently, Vclust is designed for single-contig viral genomes, so there are discrepancies when applying it to multi-contig...

Hi Valentyn, Thanks for reaching out! You are absolutely right. With nucleotide-based sequence comparisons and clustering, we can only reliably group viruses into species, or genera at best. The AAI...

Thank you for the great suggestion! In Vclust v1.1.1, we've introduced query and reference coverage (`qcov` and `rcov`) in the output, allowing for bidirectional coverage filtering to handle cases like...

Hi @apcamargo, Yes, you can do this. The only thing you need to specify in your command is the `--gani` threshold. For example, if you want to keep all edges...

There's no real reason for this - it's just how the current argument parser is set up. Right now it always expects a threshold for the metric used in clustering,...

Thank you for the kind words! Vclust can be used on genome sequences in general, but it's optimized for shorter genomes, like viruses. It's very sensitive, which is great for...

Thank you for your feedback and for using Vclust! Currently, Vclust supports only all-vs-all ANI comparisons. However, we recognize the need for a FASTA-vs-FASTA approach—it's a feature we've needed ourselves...