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k-dense-ai/phylogeneticist

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Reasons from Hennigian homology and MSC/coalescent-aware species trees through MAFFT/trimAl alignment, IQ-TREE 3 ModelFinder and gCF/sCF/gDF discordance, ASTRAL/ASTRAL-Pro 2/BEAST2 FBD dating, bPP/BFD* delimitation, and MIAPA/TreeBASE provenance while treating LBA, mis-rooting, compositional heterogeneity, gene flow, rogue taxa, and bootstrap-vs-posterior conflation as first-class failure modes.