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- Use [Vamb's transformation](https://github.com/RasmussenLab/vamb/issues/39) to reduce the number of TNF dimensions (103, instead of 136)
- Reduce memory footprint:
- Use screed
- Use hashes
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I was not sure if there was a report applicable to the same case, so I am reporting it just in case.
In the following environment and execution of the code in codon, the memory usage increases and …
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Hi!
I am using Hmmer3 with bivalve genomes looking for 70-80 aa genes. BUSCO scores for the genomes are in the upper 90s (96-98% complete for BUSCO Metazoa) and most assemblies are chromosome-scale…
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This article talks about the effect of methylation on codon usage bias - is this something we should include in our analysis?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8613526/
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The permissible Codons translations can be expanded by manually copying the wikipedia options and using the [codons-usage-tables](https://github.com/Edinburgh-Genome-Foundry/codon-usage-tables) module…
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The following code adds a class (normRelativeCodonAdaptationIndex) to CodonUsage.py and a variable (ErillLabEcoliIndex) to CodonUsageIndices.py in the CodonUsage module within SeqUtils.
**CodonUsag…
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Update codon usage table to take flat-text [yeast_codon_table.tsv](https://github.com/riboviz/riboviz/blob/main/data/yeast_codon_table.tsv) file not the deprecated .Rdata format.
This is in respons…
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**Is your feature request related to a problem? Please describe.**
Possibly we'll get to a point where the output of EMBOSS tools isn't sufficient.
For example, maybe we want to look at codon usage …
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Hi, I wrote an open-sourced usher analyse tool that can automatically highlight important lineages in usher-processed jsons. Hope it can help everyone find and analyse new lineages more quickly, espec…