Evolutionary Biology Tools
Browse all available evolutionary biology tools.
Available tools
- Adaptation Fixation Supplied Effect Term Tool Diffusion approximation for a genic selected allele, u=(1-exp(-4Nes*p))/(1-exp(-4Nes)); dominance is not included.
- Allele Age Generations Year Crosswalk Tool Calculate allele age generations year crosswalk from explicit caller-supplied inputs.
- Allele Count Frequency Residual Tool Calculate allele count frequency residual from explicit caller-supplied inputs.
- Allele Count Ploidy Denominator Label Reconcile explicit allele counts and a supplied ploidy denominator without assuming diploidy or a population model.
- Allele Missing Ploidy Support Flag Tool Count support under an explicit ploidy assumption without inferring genotype or species ploidy.
- Allele Trajectory Time Origin Offset Tool Calculate a supplied allele-trajectory time relative to explicit origin in consistent units without interpolating frequencies.
- Ancestral State Ambiguous Token Tool Serialize distinct explicitly supplied ancestral-state candidates and distinguish ambiguity from an empty unknown list without reconstructing ancestors.
- Branch Length Tip Distance Tool Sum a supplied phylogenetic path selection without inferring a tree, topology or molecular clock.
- Branch Rate Time Product Gap Tool Compare an explicit branch substitution-rate/time product with a supplied length; no clock model is fitted.
- Branch Site Substitution Opportunity Term Tool Multiply explicit branch duration, eligible site count and supplied per-site-time rate without fitting an evolutionary substitution model.
- Coalescent Generation Scale Scale explicit generations by a caller-supplied effective-population and ploidy convention without estimating either quantity.
- Coalescent Two Lineage Rate Term Tool Continuous-time Kingman pair coalescent approximation in diploid generations, not the exact finite-N geometric survival.
- Codon Site Opportunity Share Tool Normalize precomputed codon-site opportunities over explicit callable sites; no genetic code or mutation model is assumed.
- Codon Sites Zero Denominator Tool One supplied change/site ratio with zero support flagged; no substitution model or dN/dS estimator.
- Codon Synonymous Site Mask Tool Evaluate caller-verified genetic-code labels, excluded stop/unknown labels and explicitly weighted unique substitution neighbors; no universal code or mutation convention is assumed.
- dN/dS One Codon Site Count Term Tool Uncorrected changes per opportunity from supplied effective site counts; no codon-model or multiple-hit estimation.
- Evolutionary Game Fitness One Strategy Term Tool Expected strategy payoff against supplied normalized frequencies and an explicit affine payoff-to-fitness mapping.
- Evolutionary Rate Calibration Ratio Divide an explicit branch length by supplied generations without fitting a molecular clock.
- Evolutionary Replicate Founder Count Label Tool Preserve an explicitly supplied evolutionary replicate founder-count transcription and source without estimating effective population size.
- Fitness Assay Reference Competition Ratio Tool Divide supplied focal and positive reference abundance fold changes for an explicit competition ratio without log-growth or selection inference.
- Fixation Probability Neutral Copy Term Tool Neutral fixation probability equals starting allele frequency in a closed ideal population.
- Fossil Calibration Bound Type Label Tool Label an explicitly supplied fossil-calibration bound type without selecting ages, distributions or node assignments.
- Fossil Calibration Interval Width Term Tool Calculate fossil calibration interval width term from explicit caller-supplied inputs.
- Fossil Tip Sampling Age Precision Label Attach a supplied age and precision tag to a fossil tip without estimating age uncertainty or fitting a clock.
- Inbreeding Heterozygote Deficit Term Tool Nonnegative pedigree inbreeding coefficient genotype proportions; negative population F-statistics are outside this convention.
- Jukes Cantor Distance Domain Margin Tool JC69 equal-frequency equal-rate nucleotide distance; reject the p>=3/4 saturation boundary.
- Kimura Two Parameter Distance Domain Gap Tool K80 nucleotide distance with separately supplied transition and transversion mismatch fractions.
- Migration Drift Generation Expectation Tool Calculate neutral one-generation expected allele frequency after an explicit migrant fraction, with zero-mean drift excluded from the expectation.
- Migration Source Recipient Allele Gap Tool Calculate migration source recipient allele gap from explicit caller-supplied inputs.
- Molecular Clock Branch Time Factor Tool Strict-clock duration from a single branch or symmetric two-lineage divergence, with an explicit supplied rate.
- Mutation Forward Backward Balance Term Tool Forward mutation removes the focal allele and backward mutation creates it; deterministic two-allele mutation only.
- Mutation Type Reference Derived Pair Classify one explicit unambiguous DNA base substitution as unchanged, transition, or transversion.
- Out Group Root Side Flag Locate explicitly identified outgroup tips across two supplied disjoint tree sides without rerooting or inferring an outgroup.
- Phylogenetic Node Age Branch Residual Tool Ages are measured backward from the same present; inconsistent supplied node ordering remains an explicit flag.
- Phylogenetic Tip Date Root Distance Gap Tool Calculate phylogenetic tip date root distance gap from explicit caller-supplied inputs.
- Phylogeny Path Branch Sum Tool Sum an explicitly supplied tree path’s branch lengths without inferring topology.
- Phylogeny Zero Branch Contraction Flag Tool Flag exact zero-length supplied phylogeny branches under an explicit contraction switch without modifying topology or inferring polytomies.
- Population Transfer Dilution Count Return expectation-level counts under an explicit proportional transfer without rounding or simulating individuals.
- Selection Dominance Coefficient Fitness Gap Tool Relative viabilities wAA=1, wAa=1-hs, waa=1-s; overdominance and beneficial negative s remain allowed if fitnesses are nonnegative.
- Selection One Generation Allele Update Tool Diploid viability selection from Hardy-Weinberg zygotes, with explicit genotype fitnesses and no other evolutionary force.
- Selection Reference Fitness Sign Tool Explicit 1−relative-fitness sign convention, preserving negative values above the reference.
- Sequence Divergence One Site Weight Tool Calculate sequence divergence one site weight from explicit caller-supplied inputs.
- Sequence Divergence Time Unit Pair Tool Preserve an explicit sequence-divergence time transcription and unit without converting generations or calibrating a clock.
- Trait State Parsimony Cost Tool Look up one directed state-transition cost in an explicit supplied parsimony matrix.
- Tree Branch Time Unit Factor Tool Use a caller-established branch/time calibration; no molecular clock is fitted.
- Tree Tip Sampling Date Label Attach an explicit date-only sampling date and source to a phylogenetic tip without dating a tree.