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Hi,
The alignment is very fast in my case, which is based on one chromosome from different species. Thanks for the great work. I am going to build a phylogenetic tree with the alignments. So I used…
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Hello, I'm trying to run openfold multimer inference on some fasta files I have. I've been using the collabfold databases to generate the sequence alignments as these are smaller than the AF2 database…
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Since the sequence-error.tsv file has the errors for all of the alignments, knowing the map_name is helpful to filter this file.
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[Class `ProteinEmbedding`](https://github.com/scikit-bio/scikit-bio/blob/545c9859635a5b8514bd9fd599475717c533f108/skbio/embedding/_protein.py#L29-L121) implements a data structure for the storage of p…
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Since it turns out helpful for some datasets to concatenate sequences during the training, some new functionality might be desired for future training usage.
- More generic implementation for alignme…
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I have double, triple, quadruple checked that my input files are all in the correct format but I consistently get this error message which halts the run. Alignment seems to work perfectly and I have o…
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The "Inferring remaining multiple sequence alignments and gene trees" has been ended by our SLURM scheduler due to time limit. Only 6 jobs out of 35000 were still running. Is it possible to run them m…
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Hi Saskia!
Hello from Canada!
I am using Decona to genotype some amplicon data and I have run into some trouble.
First, I was able to run the example data with no problem.
But, with, my …
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Hello,
thank you for your awesome tool.
I am trying to run it ony my samples from RNA-Seq (150bp PE).
I have reads already trimmed adapters with fastp.
I am curious if "reads that failed to alig…
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### Description of feature
The current stop-codon detection in ampliseq could be improved and supplemented with frame-shift detection by implementing [MACSE](https://doi.org/10.1093/molbev/msy159). T…