Antônio Camargo

Distributed computing for the `cluster` workflow

2

Is it possible to run the `cluster` workflow across multiple nodes using the [instructions described in the Wiki](https://github.com/bbuchfink/diamond/wiki/6.-Distributed-computing)?

Difference between the `cluster`, `linclust`, and `deepclust` commands

5

Hi, I couldn’t find any information in the documentation about the differences between the `cluster`, `linclust`, and `deepclust` commands. Based on the paper’s description, I believe that the results were...

I'm comparing the HTML file generated with `convertalis` and a tabular output and I noticed that there's is a discrepancy in the reported TM-Score.  ``` query target eval alntmscore...

[BUG] Potential computation in `anvi-get-pn-ps-ratio` is incorrect

2

## Short description of the problem When anvi'o computes the potential of a given codon, it does so by evaluating whether mutations in one position (that is, with Hamming distance...

ColabFold fails when using directory with multiple .a3m as input (works for single input)

1

I'm using ColabFold via `localcolabfold` in a g4dn.12xlarge AWS EC2 instance. I have a directory with thousands of MSAs (`MSAs`) in the `.a3m` format and used it as input for...

[Suggestion] Use score calibration when identifying proviruses and plasmids

2

Just a suggestion for the [database build step](https://bioinf.shenwei.me/kmcp/database/#gtdb). Since the sample size is pretty big, it's worth using the [`--enable-score-calibration` in geNomad](https://portal.nersc.gov/genomad/score_calibration.html). This parameter substantially improves the classification accuracy and...

Deleted nodes are kept in merged.dmp

22

I'm trying to parse the GTDB r207 taxdump with [`taxopy`](https://github.com/apcamargo/taxopy) and I got the following error: ```python taxdb = taxopy.TaxDb(taxdb_dir="gtdb-taxdump/R207") ``` ``` KeyError Traceback (most recent call last) /var/folders/h4/7rmy02997p3_xb4qgjzx257c0000gp/T/ipykernel_43701/673983918.py in...

Apply cutoffs for domains

3

This is more of a question than a bug. My understanding is that when the user set a cutoff, PyHMMER will not report hits that would have `hit.included == False`....

Use hpc_hmmsearch

6

This might be outside of the scope of the project, but I thought it could be a nice addition. There's a modified version of hmmseach (https://github.com/Larofeticus/hpc_hmmsearch) that runs *way* faster...