Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

Consensus whole-genome alignments built from Progressive Cactus reduce guide-tree bias and long-branch attraction, improving split recovery in simulations and removing clear bias in Telluraves.

• Why it matters: Progressive whole-genome alignment uses a pre-specified guide tree, and guide-tree choice can distort downstream phylogenomic trees, including long-branch attraction artifacts.
• What they did: The authors generated a small set of alternative guide-tree alignments under the Progressive Cactus framework and kept only homologies consistently recovered across all alignments, then tested this in simulations and a Telluraves dataset.
• The result: In simulations, consensus alignments improve precision, better match true site-pattern frequency distributions, and recover more true splits; in Telluraves, single binary guide trees show strong bias and the consensus alignment shows no clear bias, with ~68 percent extra cost for >300 Neoaves taxa.

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