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Currently, we use Nextclade to translate from nucleotides to amino acids.
We also use it to realign the notes and amino acids, even though our nucleotides are already aligned.
This seemed fine f…
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Currently seqkit seq filters by quality based on an average quality score. However, other tools such as FASTX's fastq_quality_filter, allow the user to select how many nucleotides (as a percentage) he…
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I have a set of nucleotide sequences and I need the pairwise sequence similarity of all vs all.
I understand that one should create a fake_pref and use it to run mmseqs align. Yet, in the document…
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I'd like to rotate a genome to specified nucleotide sequence. Vertebrate mitochondrial genomes start at the `trnF-GAA` tRNA gene. The `--start_genes` option seems to require a protein sequence.
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Hi everyone,
I want to create a database with all sequences of mithocondria from insects, like this:
```
haystac database \
--mode build --mtDNA \
--query '("Insecta"[Organism] AND …
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Instead of doing global alignment on whole genome sequences, align just the searched subtype ORF sequence to the full query sequence.
The searched subtype ORF sequence should be prefixed and suffix…
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Thank you very much for your software output, which provides a new workflow for viral group research!
```
Building a new DB, current time: 03/09/2024 10:19:13
New DB name: /home/zhongpei/hard_dis…
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Hi,
I use vclust script to classify viruses into species and genera following ICTV standards.
The script of assigning viruses into putative species (tANI ≥ 95%) is:
`vclust cluster -i ani.tsv -o …
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Hi,
In the example above I can see proteins FASTA file of GCF_009025895.1_virus_proteins.faa. I want to calculate the gene abundance with virus gene sequence.Can we output the corresponding nucleo…
wfgui updated
3 months ago
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**Steps to Reproduce**
1. Switch to the Macro mode
2. Draw such a sequence of nucleosides, but it is important to manually drag each bond from AP R1 to AP R2 (do not use the “Select Connection Point…