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Read-only view of a live SciFlow workflow — this is the actual pipeline that produced these results, not a mockup. β-Lactamase Phylogeny — SciFlow. Open any stage to inspect its parameters, command, versions, inputs and outputs.
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May 01, 2026
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Created Apr 28, 2026 at 06:02
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.