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I noticed we are missing some CCHF sequences , e.g. https://www.ncbi.nlm.nih.gov/nuccore/OQ633003.1. From the ingest logs after alignment we drop from 4760 segment sequences on NCBI virus (https://www…
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I have a set of nucleotide sequences and I need the pairwise sequence similarity of all vs all.
I understand that one should create a fake_pref and use it to run mmseqs align. Yet, in the document…
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I am aligning nucleotide sequences, but veryfasttree doesn't recognize it. it ignores all a t g c n characters... What to do?
veryfasttree -nt test.aln > test.nwk
Command: veryfasttree -nt test.al…
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## Expected Behavior
easy-search should finish execution without errors
## Current Behavior
Error during pre-filter step
> Index table k-mer threshold: 0 at k-mer size 15
> Index table: …
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Hi, thanks for developing this tool
I run the script of vcf2phylip.py successfully but found the output seems to be the amino acid sequences. My code and the screenshort of my output file are as fo…
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Instead of doing global alignment on whole genome sequences, align just the searched subtype ORF sequence to the full query sequence.
The searched subtype ORF sequence should be prefixed and suffix…
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Frameshift aignments are very useful for Nanopore data, where indels are common. It can also be used for virus-related research, as [some phages have conversed programmed frameshifts](https://www.cell…
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I have been using a core genome alignment as input of grapeTree stand-alone version, but it crashes when the alignment contains too many sequences because of a memory issue (I do not have enough memor…
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The new documentation #552 contains also a revamped tutorial. However, some important sets of functionalities miss a tutorial:
- [ ] `tantan` application interface: `tutorial/application/tantan`
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### The Problem
Using the Pairwise alignment in BioFSharp.Algorithms works fine but the only implemented way to write out this alignment in a correct format is in the BioFSharp.IO.Clustal module. A…