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I am trying to fit various HMM classes (LinearRegressionHMM, or GaussianHMM) to my data but it does not let me pass `num_states=1`. For `num_states > 2`, everything works as expected. I wanted to know…
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**Is your feature request related to an existing issue or bug?**
Similar to #295, using hmm instead of a protein set.
An option like: "--hmms: Trusted HMM to first annotate from (default '')" from…
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## Short description of the problem
Even in single-contig circularized genomes, `anvi-run-hmms` does not reliably detect the 5S rRNA gene.
## anvi'o version
```
Anvi'o ......................…
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Hello,
Will the databases of HMMs ( cellular organisms and GVOG) be updated?
If I want to build my own database, how to configure it to be compatible with viralrecall?
How can I skip the prodigal…
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Was skimming Kevin Murphy's PhD thesis and found that Hierarchical HMMs (like SCFGs but with finite stack size / tractable inference) can be represented as dynamic Bayes nets, and therefore have linea…
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Hi, thanks for the great tool. I was able to get Pfam HMMs of core genes, but could not find the additional core gene HMMs from CASTs, which is mentioned in the paper: "Additional MSAs of Tn7-like cor…
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Downloading HMMER database of tax ID taxid as "4751" to /home/xly/mambaforge/envs/fun/lib/python3.8/site-packages/data/hmmer/4751
Note that this can take a long time for large taxonomic levels
cd /h…
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Hello,
I have several protein MSA's and I was wondering about the parameters to use while building HMMs. I am aware of the default command, but was curious to know if there is an advantage or use-c…
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Hi!
I'm having some trouble understanding where this can come from.
I tried to align a sequence with HMMER and filter on the e-value at 1e-05.
With HMMER, I have this result in the domtblout:
```
…
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Hi,
I have encountered problems running ViFi on EBV genome with `--disable_hmms`. The possible bug leads to 0 clusters in `output.clusters.txt` and `output.clusters.txt.range` for several samples c…