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Hi DADA2 developer,
I have a high-level conceptual question - I've seen people clustering ASVs into OTUs at certain similarity threshold for various purposed. How is that different from directly us…
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**Is your feature request related to a problem? Please describe.**
I am currently working with a dataset consisting of 20,000 sequences, and I need to perform distance-based clustering on these seq…
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# Expected Behavior
I have provided the below command
**mmseqs expandaln ./base/qdb ./uniprot/uniprotdb.index ./base/res ./uniprot/uniprotdb.index ./base/res_exp --db-load-mode 2 --expansion-mode…
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Hi developer,
Thank for developing the phammseqs!
I noticed that only mmseqs2=13.45111 is required for running phammseqs. I am encountered error associated with mmseqs2 during the clustering of …
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Hi,
I tried to run TEtrimmer with the test set, using the command:
**TEtrimmer --input_file test_input.fa --genome_file test_genome.fasta --output_dir test_output --num_threads 20 --classify_all…
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Hi,
I was checking ESM-3 structure embedding, and ESM-3 sequence embedding, and found that the distance between embeddings is very less ( 0.0001) . I am curious how ESM-3 model is pre-trained with …
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Hi,
I am not sure if this is the right place to ask this, but is there a set of options to recreate the same clustering as the ones in the weekly sequence clustering of PDB. As in this link for exam…
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Hello,
I've got a question regarding the argument `--maxaccepts` of the `vsearch` command `--cluster_fast`:
The manpage states the following about `maxaccepts`:
"_The search process sorts tar…
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Hello,
Firstly, thank you for the package! We are currently trying the tool for our transcriptomic data set.
The tool works perfectly fine in clustering mode but we encountered an error when extract…
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Dear Edgardo, Ive noticed that when adding reference sequences to alignments, prior to informed paralog filtering, in some cases these are added in the reverse direction to the extracted sequences in …