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I am attempting to download the MSA as `.pkl` packages for ~6500 accessions. I am running using the command:
`(AlphaPulldown) a05-XXXXX@a05-duke01:~/AlphaFastPPi/alphapulldown/scripts$ create_individ…
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I have a naive question about your MSA methodology. Why would the aligner choose to align short segments (1000bp) before aligning again? Perhaps I am misunderstanding the parameters to abPOA.
E…
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관리 시스템, 포인트 수집 시스템 등을 구분하여 별개의 어플리케이션으로 분리해보세요.
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As always, I assume there is a way to do this seqkit, but my fu is not strong enough to find it.
I have a BED file of positions/columns I would like to **keep** from a multiple sequence alignment.
…
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Thank you for developing such a great program! I've been using ppanggolin msa and it's been helpful. Here is the command I've been working with:
ppanggolin msa -p Pangenome_graph/pangenome.h5 --p…
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I have monomer MSAs generated for each sequence in a complex, how might I combine them to be used in a multimer structure prediction? I saw https://github.com/sokrypton/ColabFold/issues/601 discusses …
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### Description of the bug
Proteinfold - https://github.com/nf-core/proteinfold
CRITICAL The container "nf-core/proteinfold_alphafold2_msa:1.1.0" is unavailable. …
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Hi ProteinGym team,
Thank you for providing both a supervised and an unsupervised benchmark to the community. This resource makes it 100x easier to benchmark and compare models. The community was i…
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Hello,
After executing the command colabfold_batch exper/fasta-res/G0_G0.fasta exper/pdbs --num-models 5, I encountered the following errors:
```
2024-05-06 15:47:16,903 Unable to initialize back…
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Running result2msa as described in the docs
`mmseqs result2msa DB DB DB_clu DB_clu_msa`
using older versions of mmseqs2 (in e.g 2019) previously merged results to give one '`DB_clu_msa`' file …