ArticleMethods in molecular biology (Clifton, N.J.)2026
A Pipeline for Generating Datasets of Three-Dimensional Tertiary Interaction Characters for Model-Based Structural Phylogenetics.
Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- Protein Structure Characters in the Light of Phylogenetic Systematics.Genome biology and evolution · 2026Article
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3 authors.
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Abstract
Tertiary-interaction characters, termed "3Di" characters, were invented for deep structural homology search with the FoldSeek program. However, they may also be used as phylogenetic characters in model-based phylogenetic inference, just as in the Maximum Likelihood program IQ-TREE. However, to conduct such an analysis, every input amino acid (AA) sequence must be linked to a protein structure prediction file, which then must be converted to 3Di characters, and then both AA and 3Di characters need to be assembled, aligned, and joined in a partitioned data file for phylogenetic analysis. To make this process practical for medium to large datasets, we constructed a pipeline with R scripts to automate these steps. Here we present example scripts and explain the R functions used to construct a joint AA+3Di alignment file.
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