All Genetics and Molecular Biology Tools
Search every calculator, analyzer, predictor, simulator, and lab math tool on PunnettSquares.com. Use the categories to move from classical genetics to PCR, cloning, sequence analysis, oligos, population genetics, and dilution workflows.
Search by tool name, concept, molecule, formula, workflow, or lab task.
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Popular starting points
Start with these tools when you know the workflow but not the exact calculator name.
Classical Genetics
Punnett squares, inheritance patterns, Mendelian ratios, pedigrees, and trait probabilities.
12 tools
Mendelian Ratio Chi-Square Calculator
Test observed offspring counts against Mendelian ratios such as 3:1, 9:3:3:1, and trihybrid ratios.
Dihybrid Cross Probability Calculator
Calculate exact genotype and phenotype probabilities for two-trait crosses such as AaBb × AaBb.
Test Cross Calculator
Use recessive-tester offspring counts to infer whether an unknown dominant parent is homozygous or heterozygous.
Genetic Linkage Calculator
Estimate parental and recombinant offspring classes from recombination frequency and gene phase.
Sex-Linked Inheritance Calculator
Predict X-linked recessive, X-linked dominant, and Y-linked offspring outcomes by sex.
Epistasis Punnett Square Calculator
Explore modified dihybrid ratios such as 9:3:4, 12:3:1, 15:1, 9:7, and 13:3.
Mendel's Law of Segregation Simulator
Simulate allele separation, gamete formation, F1 crosses, F2 ratios, and sampling variation.
Phenotype Probability Calculator
Find the probability of a target phenotype under dominant, recessive, incomplete, or codominant rules.
Carrier Probability Calculator
Estimate autosomal recessive carrier risk, residual risk after screening, and affected-child probability.
Pedigree Analyzer Calculator
Rank likely inheritance patterns from affected relatives, sex distribution, and family transmission clues.
Trihybrid Cross Calculator
Calculate three-trait probabilities, gametes, and phenotype ratios for AaBbCc-style crosses.
Forked Line Method Calculator
Multiply independent single-gene probabilities to solve multi-trait genetics crosses faster.
Population Genetics
Allele frequencies, heterozygosity, genetic drift, selection, FST, and population structure.
12 tools
Mutation Rate Calculator
Estimate mutation rate per locus, per base pair, and per generation from observed mutant counts.
Genetic Drift Simulator
Simulate random allele-frequency change, fixation, loss, bottlenecks, and small-population effects.
Effective Population Size Calculator
Estimate Ne from sex ratio, bottlenecks, family-size variance, and heterozygosity decay.
Inbreeding Coefficient Calculator
Calculate Wright’s F from common ancestors, pedigree loops, and relationship presets.
FST Population Differentiation Calculator
Compare allele frequencies between populations using HT, HS, and fixation index FST.
Quantitative Genetics Heritability Calculator
Estimate narrow-sense and broad-sense heritability from variance components or regression data.
Selection Coefficient Calculator
Model allele-frequency change across generations using selection coefficient and dominance coefficient.
Allele Frequency Calculator
Calculate p, q, minor allele frequency, allele copies, and heterozygosity from genotype counts.
Genotype Frequency Calculator
Compare observed genotype frequencies with Hardy-Weinberg expectations such as p², 2pq, and q².
Linkage Disequilibrium Calculator
Calculate D, D′, r², haplotype frequencies, and allele frequencies for two linked markers.
Heterozygosity Calculator
Compare observed heterozygosity Ho with expected heterozygosity He for SNPs or multi-allelic loci.
Minor Allele Frequency Calculator
Calculate MAF from genotype counts, AC/AN values, or multi-allelic allele counts.
Molecular Biology
DNA sequence analysis, translation, ORFs, CRISPR guides, molecular weight, copy number, and sequence properties.
11 tools
GC Content Calculator
Measure GC percentage, AT percentage, and base composition from DNA sequences.
DNA Sequence Analyzer
Analyze DNA length, GC%, base counts, reverse complement, ORFs, and restriction sites in one dashboard.
DNA Melting Temperature Tm Calculator
Estimate primer melting temperature using sequence, salt conditions, and nearest-neighbor logic.
Codon Usage & Translation Tool
Translate coding DNA, flag start and stop codons, and count codon usage.
ORF Finder Calculator
Scan six reading frames for open reading frames, start codons, stop codons, and protein products.
DNA to Protein Translation Tool
Translate DNA in reading frames, inspect amino-acid properties, and find the longest protein product.
DNA Copy Number Calculator
Convert DNA mass concentration, length, and volume into copies per microliter or copies per reaction.
DNA Molecular Weight Calculator
Calculate molecular weight, molarity, copy number, and base composition for DNA, RNA, or oligos.
ng/µL to nM Calculator
Convert DNA, RNA, or oligo mass concentration into nanomolar concentration using length and molecular weight.
PAM Sequence Finder
Find CRISPR PAM sites such as NGG, NAG, TTTV, NNGRRT, and NGN on both DNA strands.
CRISPR Guide RNA Design Tool
Rank guide RNA candidates by PAM, GC%, strand, seed-region composition, and common screening warnings.
PCR and qPCR
PCR setup, amplicon size, qPCR efficiency, relative expression, and amplification planning.
4 tools
PCR Product Size Calculator
Find forward and reverse primer sites on a template and estimate PCR amplicon length.
PCR Master Mix Calculator
Build PCR master mix tables for commercial 2× mixes or custom reagent setups with overage.
qPCR Efficiency Calculator
Calculate amplification efficiency, slope, intercept, and R² from qPCR standard-curve data.
Delta Delta Ct Calculator
Calculate ΔCt, ΔΔCt, fold change, log2 fold change, and efficiency-corrected expression.
Cloning and Restriction
Restriction digests, ligation ratios, sticky-end compatibility, plasmids, and cloning workflows.
4 tools
Restriction Enzyme Digest Predictor
Find restriction sites, cut positions, fragment sizes, sticky ends, and blunt ends in DNA sequences.
Vector Insert Ligation Calculator
Calculate insert mass, vector volume, molar ratio, and reaction setup for DNA ligation.
Double Digest Calculator
Predict fragment sizes and reaction setup when two restriction enzymes cut linear or circular DNA.
Sticky End Compatibility Calculator
Compare restriction enzyme overhangs, blunt ends, and compatible sticky-end ligation pairs.
Oligo and Primer Tools
Primer checks, oligo resuspension, Tm, concentration, hairpins, and primer-dimer risk.
6 tools
Oligo Analyzer
Check oligo sequence properties such as Tm, GC%, length, molecular weight, and sequence composition.
Primer Dimer Calculator
Screen forward and reverse primers for self-dimers, hetero-dimers, 3′ complementarity, and GC balance.
Hairpin Calculator
Detect possible stem-loop structures in DNA or RNA oligos before PCR, qPCR, or probe ordering.
Oligo Dilution Calculator
Calculate dilution volumes for oligo stocks and working primer solutions.
Oligo Resuspension Calculator
Calculate resuspension volume for dry oligo pellets using nmol amount and target concentration.
Oligo Concentration Calculator
Convert oligo mass, amount, volume, and concentration for primer stock preparation.
Dilution and Lab Math
Stock-to-working solution dilutions, serial dilution planning, DNA dilution, and lab concentration math.
6 tools
Solution Dilution Calculator
Use C1V1 = C2V2 to dilute stock solutions to target concentration and final volume.
Serial Dilution Calculator
Plan serial dilution steps, dilution factors, transfer volumes, and final concentrations.
Dilution Ratio Calculator
Convert dilution ratios into stock volume, diluent volume, and final mixture volume.
Dilution Factor Calculator
Calculate dilution factor from initial concentration, final concentration, or serial dilution steps.
Alcohol Dilution Calculator
Calculate water and alcohol volumes needed to prepare a target alcohol percentage.
DNA Dilution Calculator
Dilute DNA stock to target ng/µL, nM, copies/µL, or per-reaction template amount.