Adrian Viehweger

Would it be possible to have a format option that writes a .delta JSON in one line (i.e. no pretty line breaks). That way you could append deltas to a...

What is the final size of the BFD, __unpacked__? I downloaded it successfully, but now am trying to allocate enough storage. https://bfd.mmseqs.com/ Thanks a lot!

Fix one set of latent representations?

1

I am new to recommender systems and would like to use latent representations for users as documented here: https://maciejkula.github.io/spotlight/factorization/representations.html#module-spotlight.factorization.representations I already trained representations (an embedding) for the items though, and...

Access to states

9

If I understand correctly, the VQ-VAE used by foldseek translates each amino acid into one of 20 "states". Do we have access to these, i.e. is it possible to get...

phylogenetic tree build fails

10

Hi, I am having problems similar to issue #690 related to building a phylogenetic tree. Housekeeping first: ```bash Anvi'o version ...............................: margaret (v5.1) Profile DB version ...........................: 29 Contigs DB...

On connectedness in metagenomic assembly graphs

2

Hi @ctb I believe it was in your blog post on spacegraphcats that you mentioned that basically all metagenomic assembly graphs are connected, and thus an approach based on graph...

Ie. does Snippy consider non-annotated, non-coding regions at all? I assume they don't appear in the .gbk reference and are thus not considered, correct? Thanks for clarifying this, Kind regards

Problem w/ branch len estimate with closely related leaves

12

In the TreeTime .nexus output I get a huge negative branch len followed by another large on for the corresponding leaves: ``` ... ((7ab5cd3e-524b-4f3e-9951-04d783bcef78:28113.25709,5abe8078-fdb6-4e90-9075-314bc4238f48:28113.15326)NODE_0000024:-28112.91947,(dd518f5c-d48a-464d-bff3-4becb51ae5d5:0.00000,0e2e43b1-45fc-4a32-b584-d4db7b91e86b:0.00000) ... ``` Is this a bug...

Allow structured output for "out-of-model" leaves

1

Thanks a lot for this great tool! TreeTime prints implausible leaves to stdout like so: ``` 263.56 TreeTime: The following tips don't fit the clock model, please remove them from...

Flagged "out-of-model" leaves are not so bad

3

TreeTime flags leaves that do not conform to the clock model like so: ``` 263.56 TreeTime: The following tips don't fit the clock model, please remove them from the tree....