Ancestral sequence reconstruction (ASR) is a foundational task in evolutionary biology, providing insights into the molecular past and guiding studies of protein function and adaptation. Conventional ASR methods rely on a multiple sequence alignment (MSA), a phylogenetic tree, and an evolutionary model. However, the underlying alignments and trees are often uncertain, and existing models typically focus on substitutions and do not explicitly account for insertion-deletion (indel) processes. Here, we introduce BetaReconstruct, a novel generative approach to ASR that harnesses recent advances in natural language processing (NLP) and hybrid transformer architectures. Our model was initially trained on large-scale simulated datasets with gold-standard ancestral sequences and subsequently on real-world protein sequences. The reconstruction requires neither MSAs nor phylogenetic trees. We demonstrate that BetaReconstruct generalizes robustly across diverse evolutionary scenarios and reconstructs ancestral sequences more accurately than maximum-likelihood-based pipelines. We additionally provide evidence that the generative-model ASR approach is also more accurate when analyzing empirical datasets. This work provides a scalable, alignment-free strategy for ASR and highlights the ability of data-driven models to capture evolutionary signals beyond the reach of traditional methods.

Illustration of ASR using BetaReconstruct. (a) The “true” evolutionary dynamics, in which the ancestral sequence “AAMM” evolved along a phylogenetic tree. The leaf sequences are the proteins: “AAM”, “AYM”, and “ATMMM”; (b) The BetaReconstruct pipeline: (Ⅰ) the unaligned protein sequences are provided as input; (Ⅱ) the protein sequences are concatenated with special characters between them; (Ⅲ) the model processes the input; (Ⅳ) the model generates the root ancestral sequence.

See Github repository: https://github.com/technion-cs-nlp/BetaReconstruct