Run date
2026-05-30 → 2026-05-31
SciFlow lab notebook · Shared read-only
Reconstruct the evolutionary history of the serine β-lactamases — the most clinically important antibiotic-resistance enzymes in Gram-negative bacteria — directly from protein sequences.
Run date
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Pipeline
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Outputs
Reconstruct the evolutionary history of the serine β-lactamases — the most clinically important antibiotic-resistance enzymes in Gram-negative bacteria — directly from protein sequences. The curated demo FASTA holds Ambler class A families (TEM, SHV, CTX-M, KPC) and Ambler class D (OXA-family) enzymes, rooted on a genuine class C AmpC cephalosporinase outgroup (E. coli K-12 AmpC, UniProt P00811). You get back a rooted maximum-likelihood tree with bootstrap support, model-selection diagnostics, and a clean alignment you can actually trust. Built for AMR surveillance teams, structural biologists mapping active-site evolution, and anyone teaching molecular evolution who wants a real-world example instead of toy data. Tips are labelled by family/class (e.g. TEM__, SHV__, KPC__, OXA__/clD__ for class D, AmpC__ for the class C outgroup) so you can verify directly that each family is recovered as a monophyletic clade — the point of a known-answer demo: confirm the pipeline gets the right answer before running it on novel sequences.
The methodology is the substance, not the topology alone. Alignment uses MAFFT (L-INS-i for accuracy at this size), trimAl removes ambiguously aligned columns under an automated heuristic, ModelFinder picks the best amino-acid substitution model by BIC, and IQ-TREE infers the tree with 1000 ultrafast bootstrap replicates and an SH-aLRT branch test, rooted on the AmpC outgroup. The output panel reports model choice, the SH-aLRT/UFBoot support distribution, alignment length retained after trimming, and class A vs class D clade recovery — because a tree without those numbers is just a picture.
3 stages, 3 completed. Each stage below lists the parameters it ran with, the software the run recorded, and the files it produced.
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No static figure could be embedded in this notebook — this run recorded no PNG/SVG output, and no interactive plot could be exported to a static image. Any figures this run produced are listed among the raw artifacts below and remain viewable in the project itself.
26 output files produced across all stages (1.8 MB total). This report is self-contained; structures and trajectories are listed below for reference.