GONE
GONE is a program for estimating the historical effective size of population from linkage disequilibrium between SNPs.
Further details are explained in:
Recent demographic history inferred by high-resolution analysis of linkage disequilibrium
Molecular Biology and Evolution, 37(12): 3642–3653, 2020 | DOI
InfoMating
InfomMating is a program for estimating non-random mating models for discrete traits.
Further details are explained in:
Multi-model inference of non-random mating from an information theoretic approach
Theoretical Population Biology, 131: 38-53, 2020 | DOI
GWEHS
GWEHS is a program aimed at screeing the NHGRI-EBI GWAS Catalog in order to find the contribution to heritability of variants for human diseases and traits.
Further details are explained in:
GWEHS: A Genome-Wide Effect Sizes and Heritability Screener
Genes, 10(8): 558, 2019 | DOI
Metapop2
Metapop2 is a software for management of subdivided populations in conservation programs. Using molecular marker data or pedigree information, the software determines the optimal contributions (i.e. number of offspring) of each individual, the number of migrants, and the particular subpopulations involved in the exchange of individuals in order to maintain the largest level of gene diversity in the whole population with a desired control in the rate of inbreeding. Restrictions can be introduced for the total number of migrants, and the mating of particular pairs and their contribution. A full genetic diversity analysis of the population is also carried out.
Further details are explained in:
Metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity
Molecular Ecology Resources, 19: 1095-1100, 2019 | DOI
MateSim
MateSim is a program that uses Monte Carlo simulation for the generation of mating tables.
Further details are explained in:
MateSim: Monte Carlo simulation for the generation of mating tables
Biosystems, 171: 26-30, 2018 | DOI
Myriads
Myriads is a software package for P-value-based multiple testing that also implements a dependence test and P-value simulation.
Further details are explained in:
Myriads: P-value-based multiple testing correction
Bioinformatics, 34(6): 1043–1045, 2018 | DOI
AFLPMax
AFLPMax is a program aimed at finding the optimal number of AFLP (Amplified Fragment Length Polymorphism, Vos et al. 1995) sampled bands needed to reconstruct an accurate and well-supported AFLP-based phylogeny. Given a reference tree obtained a priori by any phylogenetic inference method and any source of information, AFLPMax provides the optimal number of AFLP bands that would be needed to reconstruct that tree with accuracy and, therefore, it is a tool useful to optimize resources and work for the reconstruction.
Further details are explained in:
AFLPMax: a user-friendly application for computing the optimal number of AFLP markers needed in phylogenetic reconstruction
Molecular Ecology Resources, 12(3): 566-569, 2012 | DOI
FAMSPHERE
FamSphere is a easy to use C++ computer program that implements a distance-based method to allocate families based on co-dominant molecular marker information.
Further details are explained in:
FamSphere: A computer program for parental allocation from known genotypic pools: Program note
Molecular Ecology Notes, 7(2): 213-216, 2007 | DOI
JMATING
Software to calculate in an easy and intuitive way the most important sexual isolation and sexual selection estimates.
It also allows for efficient bootstrapping of the estimators for testing hypothesis about sexual selection and isolation.
Further details are explained in:
JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data
BMC Evolutionary Biology, 6: 40, 2006 | DOI