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I searched for issues related to the function 'ggtree::msaplot' and found this website:
https://www.r-bloggers.com/2016/08/ggtree-for-microbiome-data/
I am unable to get this line working:
msaplo…
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https://yuzhenpeng.github.io/2019/11/29/multiple-sequence-alignment/
multiple sequence alignment
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The gene alignment step can take a long time to complete. Is it possible to add functionality to output the unaligned gene sequences to later align batches of them across a computing cluster? The pira…
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Hello there, thank you for this really great tool.
Lately, I am trying to perform an orthofinder analysis using 38 species as input, but I am having the following problem.
After the diamond anal…
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Hi again,
I have another question, is there a way to retain the reads that map to each reference taxon? I have looked at the various options for output-type and do not see the option to output the …
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This is a proposal for a new term "Manual motif inference based on multiple sequence alignment" as used in the CollecTF database (www.collectf.org). Manual motif inference based on multiple sequence a…
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This is a proposal for a new term "Manual motif instance prediction based on multiple sequence alignment" as used in the CollecTF database (www.collectf.org). Manual motif instance prediction based on…
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Hi
First of all Great work, just a question :
is this possible to pass a batch of protein sequences to the `alignment_runner.run(fasta_path, local_alignment_dir)` in the run_pretrained_openfold…
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I have a multiple sequence alignment with gene IDs as the names of the sequences (.fa file). I also have a metadata excel table with two columns (gene IDs and taxonomic names). I want to rename (repla…
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Hi,
I want to know if foldseek can output multiple structural alignment generated using 3Di as aligned 3Di alphabet sequences in Fasta format and not aligned amino acid sequences of the proteins.…