Journal: Genome Biology and Evolution

Article Title: Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes

doi: 10.1093/gbe/evaf109

Figure Lengend Snippet: Graphical illustration of the Unicore workflow. a) The input species proteome, represented as amino acid sequences, is translated to 3Di alphabets (denoted by underscores) using the ProstT5 language model. These 3Di sequences are clustered with Foldseek to group structurally homologous proteins. Structural core genes are identified from these clusters by selecting those conserved as a single-copy in more than a specified proportion of the input species. b) FoldMason is used to construct MSTAs for each structural core gene cluster. These alignments are then converted back into amino acid sequences, enabling conventional evolutionary model-based maximum likelihood phylogenetic inference. Finally, a species phylogenetic tree is generated from the concatenated MSAs.

Article Snippet: By applying the ProstT5 protein language model to the input proteomes to obtain their 3Di structural strings, Unicore saves over three orders of magnitude in runtime compared to a full 3D prediction.

Techniques: Construct, Generated

Journal: Genome Biology and Evolution

Article Title: Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes

doi: 10.1093/gbe/evaf109

Figure Lengend Snippet: Graphical illustration of the Unicore workflow. a) The input species proteome, represented as amino acid sequences, is translated to 3Di alphabets (denoted by underscores) using the ProstT5 language model. These 3Di sequences are clustered with Foldseek to group structurally homologous proteins. Structural core genes are identified from these clusters by selecting those conserved as a single-copy in more than a specified proportion of the input species. b) FoldMason is used to construct MSTAs for each structural core gene cluster. These alignments are then converted back into amino acid sequences, enabling conventional evolutionary model-based maximum likelihood phylogenetic inference. Finally, a species phylogenetic tree is generated from the concatenated MSAs.

Article Snippet: Unicore leverages predicted 3Di sequences from the ProstT5 model and linear-time comparison methods ( ) to accelerate large-scale proteome analysis.

Techniques: Construct, Generated

Journal: bioRxiv

Article Title: Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes

doi: 10.1101/2024.12.22.629535

Figure Lengend Snippet: Graphical illustration of the Unicore workflow. (a) The input species proteome, represented as amino acid sequences, is translated to 3Di alphabets (denoted by underscores) using the ProstT5 language model. These 3Di sequences are clustered with Foldseek to group structurally homologous proteins. Structural core genes are identified from these clusters by selecting those conserved as a single-copy in more than a specified proportion of the input species. (b) Foldmason is used to construct multiple structural alignments (MSTAs) for each structural core gene cluster. These alignments are then converted back into amino acid sequences, enabling conventional evolutionary model-based maximum likelihood phylogenetic inference. Finally, a species phylogenetic tree is generated from the concatenated MSAs.

Article Snippet: By applying the ProstT5 protein language model to the input proteomes to obtain their 3Di structural strings, Unicore saves over three orders of magnitude in runtime compared to a full 3D prediction.

Techniques: Construct, Generated