Structure-Aware Amino Acid Substitution Models for Five Taxonomic Groups

Processed data supporting analyses of structure-aware amino acid substitution models. The dataset includes inferred Q matrices, cleaned multiple sequence alignments, and structural annotation files for five taxonomic groups, totaling 279.5 MB. It was authored by Peter Wayne Goodman and last updated on 2026-05-28.

Use Cases

• Benchmarking structure-aware substitution models based on the provided Q matrices for surface and buried residues.
• Training new phylogenetic models using the cleaned and filtered multiple sequence alignments.
• Analyzing site-specific evolutionary rates based on the NEXUS-formatted structural annotation files.
• Reproducing analyses from the associated research using the scripts in the linked GitHub repository.

Strengths

• Includes data for five distinct taxonomic groups, allowing for comparative analysis.
• Provides 279.5 MB of processed data, including inferred matrices, alignments, and annotations.
• Associated GitHub repository contains the scripts used for generation and analysis, supporting reproducibility.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for specific modeling tasks.
• Description metadata is limited; actual data quality requires manual inspection after download.

Provenance

Source

figshare

Collection Method

Data was processed and inferred to support specific research analyses, as detailed in the associated publication.

Freshness

Last updated 2026-05-28 16:56:20; freshness should be verified.