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**Problem:** SARS-CoV2 genomes already downloaded have ambiguity codes in them. Our pipeline needs to handle this in some way.
**Simon Heumos:**
Sequences like 'Y' or 'K' are encoding a nucleotid…
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Hi,
Attempting to use Corason within the "tutorial" from BiG-SCAPE/Corason site using TauD and selected genomes (https://bigscape-corason.secondarymetabolites.org/tutorial/), on a Windows 11 Opera…
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Author Name: **Dmitry Samborskiy** (Dmitry Samborskiy)
Original Redmine Issue: 2280, https://redmine.open-bio.org/issues/2280
Original Date: 2007-04-27
Original Assignee: Bioperl Guts
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Hi Al…
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As of Biopython 1.71, *Bio.SeqIO now supports reading and writing two-line-per-record FASTA files under the format name "fasta-2line", useful if you wish to work without line-wrapped sequences.*
Re…
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## Context
The increasing amount of data has shed light on limitations of the current file-based approach (#789). There have been solutions implemented, mostly in `augur filter`, to improve memory …
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I would like to propose the idea for "Pipeline for customized phylogeny based on user provided gene/protein sequence(s) using Open Tree of Life data".
Suppose a researcher has newly sequenced a gene…
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Hi Marco,
Thanks so much for making a really great package. I am going though the specified commands using the example Acinetobacter data provided in the supplemental data 3 from https://doi.org/10…
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Hello,
I'm working on a program that runs BLAT between two files with protein sequences and parses the output psl file using Bio.SearchIO.BlatIO. I stumbled an issue where parsing the psl produces …
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Greetings, trying to build default genomic data-bases used to run kraken2 on an HPC cluster. The database location is set for my scratch directory, which i believe has 15TB of space available. Regardl…
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@sammyjava has a `5.1.0.4-model-changes` branch that adds support for Intermine version 5.1.0.4, which is required to integrate the [trait association search web component](https://legumeinfo.github.…