-
In using normalizer, we ran into an issue with p. prediction/generation for two delins that involved more than one codon. In both cases, Normalizer normalized the c. as two dels separated by a single …
-
According to README, user has to provide a FASTA or Genbank file to seed the simulation with a root sequence. However, we *should* be able to generate a root sequence given a configuration of the evo…
-
Both Codon and [Triton](https://github.com/openai/triton) can generate CUDA kernels. What are the differences between the two when it comes to GPU programming?
Thanks!
PS. This may be something …
-
When an alignment has a stop codon followed by gaps is detected as an early stop codon.
example:
```
>1
ACGTCA---TAG
>2
AC----TAA---
```
The `TAA` stop codon in the second sequence is a term…
-
Hi, to start I have really enjoyed `eukcc`, so thank you!
I have recently discovered that if my protein files include stop codon marks (`*`) my job fails with the following error message:
```
…
-
i have got some codon degeneracy matrix and used iqtree for tree inference. I found that it just followed as amino acid data when modelfinder progress. Can someone tell me the truth? Many thanks!
-
Hello,
I have a request that should enhance the utility of DNA Chisel for codon optimization.
When selecting Codon Usage Tables for species [not included](https://github.com/Edinburgh-Genome-Fou…
-
The bioconda version (1.0.2) is obsolete, as has issues in it preventing it from optimising CAI as intended. E.g. maximal CAI optimisation does not lead to a CAI of 1.
h-ahl updated
1 month ago
-
Why does a transcript sequence assembled by Trinity.fasta have many stop codons in the middle?
-
Dear Thomas,
I am trying to run ProtHint on an assembly of a plant genome (~13k contigs, ~1.9Gbp). As a protein set, I used the OrthoDB Viridiplantae set (https://v100.orthodb.org/download/odb10_pl…