A new tree-conditioned edit-flow model for ancestral sequence reconstruction achieves reasonable accuracy on substitution-only evolved sequences and superior localization of changes on natural indel-rich sequences.
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0.Systematic Biology, 59(3):307–321
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BEAGLE 4.1 adds gradient evaluation algorithms and hardware-specific implementations for CPUs and GPUs, reporting up to 10-fold speedups for codon models and 4-fold for multi-core CPUs over single-threaded baselines.
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Tree-Conditioned Edit Flows for Ancestral Sequence Reconstruction
A new tree-conditioned edit-flow model for ancestral sequence reconstruction achieves reasonable accuracy on substitution-only evolved sequences and superior localization of changes on natural indel-rich sequences.