SNPio Documentation

SNPio is a Python package designed for efficient input/ output, filtering, encoding, and analysis of SNP (Single Nucleotide Polymorphism) data. It provides tools for reading, filtering, analyzing, and visualizing SNP data from various formats. It is intended to be efficient, intuitive, and easy to use for researchers working with genetic data.

This documentation provides an overview of the package’s modules, classes, and functions, along with examples and usage guidelines.

SNPio is described in Martin et al. (2026). See Publication, Citation, and Reproducibility for the complete citation, OSF reproducibility repository, and supported PyPI, conda, and Docker distributions.

Contents:

• Getting Started
  • Installation
  • Importing SNPio
  • Reading Genotype Data
  • The GenotypeData Object
  • Specifying Populations
  • force_popmap Behavior
  • Supported Missing Data Characters
  • Population Map File Format
  • Writing Genotype Data to File
  • Next Steps
• Filtering Genotype Data with NRemover2
  • Basic Example
  • Filtered-data consistency
  • Filtering with exclude_heterozygous
  • Key Filtering Methods
  • Threshold Grid Search
  • Filtering Visualizations
  • Best Practices
  • Next Steps
• Encoding Genotype Data
  • Importing GenotypeEncoder
  • Encoding Formats
  • Reversing the Encoding
  • Use Cases
  • Next Steps
• Population Genetic Analysis
  • Basic Usage
• Allele Summary Statistics
  • Example
  • Output
  • Nei’s (1972) Genetic Distance
  • Weir & Cockerham Fst (Distance Matrix)
  • Unbiased Linkage Disequilibrium from Unlinked SNPs
  • D-Statistics (Patterson, Partitioned, DFOIL)
  • Fst Outlier Detection
  • AMOVA (Experimental)
  • PopGenStatistics Method Summary
  • Next Steps
• MultiQC Report Generation
  • Basic Example
  • Report Contents
  • Custom Report Location
  • Exporting Report Data
  • Integration with Analysis Pipeline
  • Next Steps
• Tree Parsing and Phylogenetic Analysis (Experimental)
  • Basic Example
  • Reading and Drawing Trees
  • Saving Trees to File
  • Tree Editing and Analysis
  • Distance Matrix and Evolutionary Rates
  • Input File Notes
  • Experimental Status
  • Example Use Case: Extracting a Subtree and Saving to Newick
  • Conclusion
• References
• SNPio Tutorial
  • Install SNPio
  • Load the example data
  • Run unphased LD and recent \(N_e\)
  • Inspect the population summary
  • Inspect reproducibility metadata
  • Generated outputs
  • Coordinate-free or pre-pruned input
  • Sensitivity checks before reporting
  • Validation and citation
• Unphased Linkage Disequilibrium and Recent Effective Size
  • What SNPio estimates
  • Finite-sample unbiased polynomial algorithm
  • Selecting genuinely unlinked pairs
  • Aggregation, pair sampling, and parallel execution
  • Bootstrap confidence intervals
  • Python API
  • Returned result and generated files
  • MultiQC panels
  • Plot colors, scales, and diagnostic warnings
  • Interpretation and limitations
  • Validation resources
• Validating Linkage Disequilibrium Estimates
  • Validation code and evidence locations
  • Validation hierarchy
  • Curated validation results
  • Fast deterministic validation
  • Robust all-layer runner
  • Forward-time calibration
  • Published island-fox benchmark
  • Target-dataset pair convergence
  • What constitutes strong validation?
• Publication, Citation, and Reproducibility
  • How to cite SNPio
  • Publication files
  • OSF reproducibility repository
  • Installation distributions
• Command-Line Workflow
  • Basic invocation
  • Input and filtering options
  • Parallelism, plots, and resampling
  • LD and recent effective-size options
  • D-statistic options
  • Fst outlier and run-control options
  • Generated outputs
  • Equivalent module invocation
• Changelog
  • Unreleased
  • Version 1.7.3 (2026-07-23)
  • Version 1.7.2 (2026-07-23)
  • Version 1.7.1 (2026-07-23)
  • Version 1.7.0 (2026-07-23)
  • Version 1.6.16 (2026-05-20)
  • Version 1.6.15 (2026-05-20)
  • Version 1.6.14 (2026-05-20)
  • Version 1.6.11 (2025-10-05)
  • Version 1.6.10 (2025-10-05)
  • Version 1.6.9 (2025-10-05)
  • Version 1.6.8 (2025-10-03)
  • Version 1.6.7 (2025-09-25)
  • Version 1.6.6 (2025-09-24)
  • Version 1.6.5 (2025-09-24)
  • Version 1.6.4 (2025-09-20)
  • Version 1.6.3 (2025-09-20)
  • Version 1.6.2 (2025-09-15)
  • Version 1.6.1 (2025-09-01)
  • Version 1.6.0 (2025-07-24)
  • Version 1.5.5 (2025-07-07)
  • Version 1.5.0 (2025-07-04)
  • Version 1.3.21 (2025-06-16)
  • Version 1.3.15 (2025-06-14)
  • Version 1.3.14 (2025-06-12)
  • Version 1.3.13 (2025-06-12)
  • Version 1.3.11 (2025-06-12)
  • Version 1.3.9 (2025-06-11)
  • Version 1.2.1 (2025-01-06)
  • Version 1.2.0 (2024-11-07)
  • Version 1.1.3 (2024-10-25)
  • Version 1.1.0 (2024-10-08)
  • Version 1.0.5 (2023-09-16)
  • Version 1.0.4 (2023-09-10)
  • Version 1.0.3.2 (2023-08-28)
  • Version 1.0.3 (2023-08-27)
  • Version 1.0.2 (2023-08-13)

API Reference:

• API Reference
  • snpio.VCFReader
  • snpio.PhylipReader
  • snpio.StructureReader
  • snpio.GenePopReader
  • snpio.NRemover2
  • snpio.PopGenStatistics
  • snpio.LinkageDisequilibriumResult
  • snpio.GenotypeEncoder
  • snpio.Plotting
  • snpio.TreeParser
  • snpio.SNPioMultiQC
• snpio.io package
  • snpio.io.vcf_reader.VCFReader
  • snpio.io.phylip_reader.PhylipReader
  • snpio.io.structure_reader.StructureReader
  • snpio.io.genepop_reader.GenePopReader
• snpio.filtering
  • snpio.filtering.nremover2.NRemover2
• snpio.popgenstats package
  • snpio.popgenstats.pop_gen_statistics.PopGenStatistics
  • snpio.popgenstats.linkage_disequilibrium.LinkageDisequilibriumResult
  • snpio.popgenstats.linkage_disequilibrium.LinkageDisequilibrium
• snpio.analysis
  • snpio.analysis.genotype_encoder.GenotypeEncoder
  • snpio.analysis.tree_parser.TreeParser
• snpio.plotting package
  • snpio.plotting.plotting.Plotting