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Dear Osamu, @ogotoh
I followed your instruction from [issue 77](https://github.com/ogotoh/spaln/issues/77) to successfully map and align protein sequences to a genome. However, the "match format"…
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Hi,
I'm trying to replicate analysis completed back in 2013 using an older version of Hyphy. The analysis I'd like to run would includes estimating distances for Fst using an ML approach under a G…
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Hi, I'm trying to do a n ANI Matrix usign this command line. but i have some problems.
I used this command line https://github.com/asadprodhan/Average-Nucleotide-Identity-ANI-analysis.git and I fol…
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**Description**
**Sub-lineage of:** JN.1.4
**Earliest sequence:** 2024-9-20, Hong Kong, EPI_ISL_19464534
**Most recent sequence:** 2024-10-10, Hong Kong, EPI_ISL_19498393
**Continents circulatin…
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The new version of CUDASW 4.0 claims to support only protein chains.
What needs to be done to be able to search in the nucleotide database?
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## Expected Behavior
Hello, when I run mmseq_gpu on my own data set, this error is reported. Is there any command restriction to prevent it from reporting such an error?
## Context
stdout:
sear…
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Hi, thanks for developing this tool
I run the script of vcf2phylip.py successfully but found the output seems to be the amino acid sequences. My code and the screenshort of my output file are as fo…
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Hello. I am trying to analyze a DNA sequence fasta file for COGs. Is it possible to use a fasta file for that purpose? The file is aligned with gene NCBI IDs.
Example command:
`BioSAK COG2020 -m N…
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## Expected Behavior
mmseqs createindex "colabfold_envdb_202108_db"
## Current Behavior
Not enough memory to keep dbreader/write in memory!
Memory limit: 14845796352 dbreader/writer need: 2275…
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Hi!
Great work with FANTASIA! I have been testing it in various scenarios. When applying to metagenomic eukaryotic data, I rather often have incomplete genes predicted (but tool such as AUGUSTUS ma…