Population
- qps 1.0 – Simulate Populations evolving on a two-dimensional Continuum
- AgeStructure 1.0 – Estimate Effective Size & Generation Interval of Population with overlapping Generations
- GENOMEPOP 2.6.2 – Evolve Populations of Genomes under complex Evolution Models and Demography
- Genepop 4.2 – Population Genetics Software Package
- varLD 1.0 – Comparison of Variation in Linkage Disequilibrium between Population
- ProSeq 3.5 – Sequence Editing and Population Genetics Analysis
- Mosy 1.1 – Detect Recent Selective Sweep & Estimate its Parameters in Population with varying size
- Populations 1.2.32 – Population Genetic Software
- PHASEBOOK 2.4 – Phasing Marker Genotypes using familial (LINKPHASE), population information
- imappingfamily – QTL Detection in a Population with Family Structure
- LAMARC 2.1.8 – Maximum Likelihood & Bayesian Estimation of Population Parameters
- TreesimJ 0.7 – Population Genetics Simulator Program
- SENDBS – Computes Average Nucleotide Substitutions within and between Populations
- WhichRun 4.1 – software for Assigning Individuals to Populations
- SAMOVA 1.0 – Define the Genetic Structure of Population
- SIMCOAL 2.1.2 – Simulation of Molecular data in interconnected Populations with Arbitrary Demography
- SGS 1.0d – Analysis of Spatial Genetic and Phenotypic Structures of Individuals and Population
- Molkin 3.0 – Genetic analysis of Populations using Molecular Coancestry Information
- StreamTree 20090303 – Map Genetic Differences between Populations
- MM-Dist 20070306 – Estimating the Distribution of Genotypic Differences (mismatches) between Individuals in a Population
- PSAT – Population Stratification Association Test
- POPSIM 2.13 – Population Simulation program
- EasyPop 2.0.1 – Simulate Population Genetics Datasets
- Margarita – Infer Genealogies from Population Genotype data
- ROADTRIPS 1.2 – Case-Control Association Testing with Partially or Completely Unknown Population and Pedigree Structure
- Overpaint 0.2 – Joint Estimation of Gene Conversion Rates and Mean Conversion Tract Lengths from Population SNP data
- RecBlock – Find Optimal Mosaic Pattern for Recombinant Population SNP Sequences
- EIGENSOFT 4.2 – Population Structure , Eigenanalysis & Stratification
- DistMiss 1.0 – Compute Matrix of Genetic Distances between Populations
- Rarefac – Option of Rarefaction and Partitioning of Allelic Richness within Populations
- HIPPO 1.0/ AEML 1.0 – Estimate Population Haplotype Frequencies from Pooled SNP data
- SelSim 2.1 – Simulate Population Genetic Data with Selection and Recombination
- TetraploidMap 1.0.6 – Calculate Linkage Maps for Autotetraploid Populations
- Adapt-A-Rate 1.0 – Estimate the Rate of Adaptive Fixation in a Population
- Multilocus 1.3b – Analysis of Multi-locus Population Genetic Data
- DISTANCE – Plot Genetic Distances between Populations
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