# LOD Score Calculator (linkage analysis) Two-point linkage LOD scores from recombinant/non-recombinant meioses: θ̂ = r/N, Zmax, LOD at fixed θ, LOD curve table, Morton thresholds (Z≥3 linkage, Z≤−2 excluded). Derived from Morton 1955, Ott 1999, Griffiths, StatPearls. Educational use only. > Canonical page: https://elysiatools.com/en/tools/lod-score-calculator - **Category:** Education - **Keywords:** lod score, lod score calculator, linkage analysis, genetic linkage, recombination fraction, theta estimate, logarithm of odds, gene mapping, two-point linkage, mendelian genetics, genetics ## Overview The LOD Score Calculator performs educational two-point linkage analysis from recombinant and non-recombinant meioses. It estimates the recombination fraction, calculates the maximum LOD or LOD at a fixed theta, and interprets results using classic linkage thresholds. ## Inputs - **Theta Mode** (select): Report the maximum LOD at θ̂ = r/N, or evaluate the LOD at a fixed θ. - **Recombinant count** (number): Number of recombinant meioses observed (r). - **Non-recombinant count** (number): Number of non-recombinant meioses observed. - **Recombination fraction θ** (number): Recombination fraction at which to evaluate the LOD in fixed-θ mode (0 < θ < 0.5). - **Decimal Places** (number) ## When to use - Estimate the recombination fraction and maximum LOD from observed recombinant and non-recombinant meioses. - Evaluate evidence for or against linkage at a specific recombination fraction theta. - Use classic LOD thresholds to support, exclude, or assess uncertainty about two-point genetic linkage. ## How it works - Choose Maximum LOD to estimate theta as the recombinant count divided by the total meioses, or choose fixed-theta mode. - Enter the recombinant count and non-recombinant count from the linkage sample. - In fixed-theta mode, enter a theta value between 0 and 0.5 for evaluation. - The calculator returns JSON with the estimated or selected theta, LOD result, and linkage conclusion, using the requested decimal precision. ## Use cases - Teaching Mendelian genetics, recombination fractions, and logarithm-of-odds calculations. - Checking two-point linkage exercises with known recombinant and non-recombinant meiosis counts. - Comparing linkage evidence at an estimated theta versus a fixed genetic distance. ## Frequently asked questions ### What does a LOD score measure? A LOD score is the base-10 logarithm of the odds comparing a linkage model at a chosen theta with no linkage at theta = 0.5. ### How is the estimated recombination fraction calculated? The maximum-likelihood estimate is theta-hat = r/N, where r is the recombinant count and N is the total of recombinant and non-recombinant meioses. ### What does a LOD score of 3 or higher mean? A LOD score of at least 3 is classic evidence supporting linkage, corresponding to odds of at least 1000:1. ### What does a LOD score of -2 or lower mean? A LOD score of -2 or lower is classic evidence against linkage at the evaluated theta. ### Is this calculator intended for clinical diagnosis? 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