MKado

Contents:

  • Installation
    • Requirements
    • Installing with pip
    • Installing with uv (Recommended)
    • Development Installation
    • Running Tests
    • Verifying Installation
  • Getting Started Tutorial
    • Prerequisites
    • The McDonald-Kreitman Test
    • Your First MK Test
    • Interpreting Results
      • Neutrality Index (NI)
      • Alpha
    • Asymptotic MK Test
      • Determining Derived Allele Frequency
      • The Asymptotic Method
      • Model Selection
    • Allele Polarization
      • Polarization in Standard MK and Asymptotic Tests
    • Polarized MK Test
      • Polarizing Fixed Differences
      • Polarizing Polymorphisms
      • Interpreting Polarized Results
      • Why Use Polarization?
    • Frequency Filtering Options
      • --min-freq (Standard MK, Polarized MK, and α_TG)
      • --no-singletons (Standard MK, Polarized MK, and α_TG)
      • --freq-cutoffs (Asymptotic MK test)
      • Key Differences
    • Genetic Code Tables
      • Available Codes
    • Output Formats
    • Working with VCF Data
    • Working with Ortholog Alignments (OrthoMaM-style projection)
    • Next Steps
    • References
  • Batch Processing Workflow
    • Basic Batch Processing
    • Per-gene vs Aggregated Modes
    • File Organization
      • Combined File Mode (Recommended)
      • Separate Files Mode
    • Asymptotic Batch Analysis
      • Aggregated Analysis
      • Asymptotic Alpha Plot
      • Per-Gene Analysis
      • Tarone-Greenland Alpha (α_TG)
    • Parallel Processing
    • Output Formats
      • Pretty Print (Default)
      • Tab-Separated Values
      • JSON
    • Multiple Testing Correction
    • Volcano Plots
      • Plot Features
      • Interpreting the Plot
    • File Filtering
    • Advanced Options
      • Frequency Bins
      • Reading Frame
    • Example Workflow
    • References
  • VCF Input Mode
    • Required Input Files
      • --vcf : Ingroup VCF
      • --outgroup-vcf : Outgroup VCF
      • --ref : Reference FASTA
      • --gff : GFF3 Annotation
    • Basic Usage
    • Gene Selection
    • Analysis Modes
      • Frequency Filtering
      • Additional Options
    • How It Works
      • Polymorphism Extraction
      • Divergence Extraction
    • Edge Cases
    • Parallel Processing
    • Output Formats
      • TSV Output Columns
      • Multiple Testing Correction
      • Plotting
    • Preparing Your Data
    • Comparison with FASTA Mode
  • Asymptotic MK Test
    • Background
    • The Key Insight
    • The α(x) Formula
    • SFS Construction: At-x vs Above-x
    • Determining Derived Allele Frequency
    • Model Fitting and Selection
    • Usage
      • Single Gene Analysis
      • Batch Analysis (Aggregated)
      • Batch Analysis (Per-Gene)
      • Confidence Interval Method
    • Output
    • The Alpha(x) Plot
    • Frequency Cutoffs
    • Comparison with Other Methods
    • When to Use Asymptotic α
    • Interpreting Results
    • References
  • Imputed MK Test
    • Background
    • The Key Insight
    • The Imputation Formula
    • DFE Fractions
    • Usage
      • Single Gene Analysis
      • Batch Analysis (Aggregated)
      • Batch Analysis (Per-Gene)
      • Bootstrap Confidence Intervals
    • Output
    • Comparison with Other Methods
    • When to Use the Imputed MK Test
    • Interpreting Results
    • Choosing the DAF Cutoff
    • Reference
  • Tarone-Greenland Alpha (α_TG)
    • Background
    • The NI_TG Formula
    • Usage
      • Frequency-Threshold Correction (FWW)
    • Output
    • Comparison with Other Methods
    • When to Use α_TG
    • Reference
  • Direction of Selection (DoS)
    • Background
    • The DoS Formula
    • Interpretation
    • Advantages over NI
    • Output
    • Example Calculation
    • Edge Cases
    • Reference
  • Omega Decomposition (ω, ω_a, ω_na)
    • Background
    • The decomposition
    • Site counting
    • When ω_a / ω_na are reported (and when they are not)
    • Confidence intervals
    • Edge cases
    • References
  • File Formats and Input Requirements
    • FASTA Format
    • Alignment Requirements
      • Codon Alignment
    • Sequence Naming Conventions
    • Ingroup and Outgroup
      • Definitions
      • Selection Guidelines
    • Handling Special Cases
      • Gaps
      • Stop Codons
      • Ambiguous Bases
    • Common Problems
      • Alignment Not in Frame
      • Wrong Species Pattern
      • Unequal Sequence Lengths
    • VCF Mode Input Files
      • VCF Files
      • Reference FASTA
      • GFF3 Annotation
    • Example Data
  • Python API Reference
    • Quick Start
    • Core Classes
      • SequenceSet
      • GeneticCode
      • AlignedPair
    • Analysis Functions
      • Standard MK Test
      • Asymptotic MK Test
      • Imputed MK Test
      • Polarized MK Test
    • Usage Examples
      • Working with SequenceSet
      • Running MK Tests
      • Asymptotic Analysis
      • Batch Processing
      • Generating Volcano Plots
      • Generating Asymptotic Plots
    • Plotting Functions
      • create_volcano_plot()
      • create_asymptotic_plot()
MKado
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© Copyright 2025, Andrew Kern.

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