tooluniverse-phylogenetics
Phylogenetics and Sequence Analysis
PhyKIT, Biopython, and DendroPy for alignment/tree analysis, evolutionary metrics, and comparative genomics.
LOOK UP, DON'T GUESS
When uncertain about any scientific fact, SEARCH databases first.
When to Use
FASTA/PHYLIP/Nexus/Newick files; treeness, RCV, DVMC, evolutionary rate, parsimony sites, tree length, bootstrap; group comparisons (Mann-Whitney U); tree construction (NJ/UPGMA/parsimony); Robinson-Foulds distance.
BixBench: 33 questions across bix-4, bix-11, bix-12, bix-25, bix-35, bix-38, bix-45, bix-60.
NOT for: MSA generation (MUSCLE/MAFFT), ML trees (IQ-TREE/RAxML), Bayesian (MrBayes/BEAST).
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