Update 07232026 Meeting notes.md - #4
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danbhrgthb wants to merge 44 commits into
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kescobo
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Jul 30, 2026
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| [waafle_env.yaml] | ||
| ```yaml | ||
| `waafle_env.yaml` |
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| `waafle_env.yaml` | |
| # `waafle_env.yaml` |
The # at the beginning here will turn it into a comment in YAML - if you included that text inside the file, it would cause a parse error.
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Very curious to see how this goes!
kescobo
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Aug 17, 2026
| First, we gotta familiarize ourselves with the genomes: the genomes live within dogen (path: lab/binfanctious/genomes/data/bilgenome, a folder of FASTA files), and a results folder holds annotated proteins (GFF files). I’ll choose around 10 genes to look at and see how they are labeled and what is within each of their folders | ||
| Second, we gotta generate proper alignments: For each target gene, gather its version (ortholog) from every genome, align them, and eyeball the alignment to make sure it is clean. | ||
| Multiple Sequence Alingment (MSA) = all sequences aligned to each other simultaneously | ||
| Tools: Clustal Omega |
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I forgot about mafft - that's another good option for MSA
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