QGSP Softwares¶

Upload your datasets¶

• using the tool Upload File
• using your favorite FTP client software (FileZilla)
• using command line under Linux session

Select a tool on left menu and process your data!¶

• Convert Formats
  • Convert QTLMap genotype/data/genealogy format in the GS3 format conversion...
  • Convert the default Illumina Genome Studio output format in the QTLMap genotype format
  • Convert GS3 phenotype/genotype in the Simple BayesCPi format
  • Convert the AIPL genotype format to MPE genotype format
  • Convert the UGA genotype format to MPE genotype format
• Genotypes Tools
  • Mendelsoft
  • MendelSoft - QTLMap format
  • MendelSoft - GS3 format
• Genealogy Tools
  • Ped Util Preparation of a pedigree file for the other PEDIG programs
  • Verif Ped Pedigree checking
  • ngen computes the average number of known ancestors, the percentage of known ancestors per generation, and the number of equivalent complete generations traced
  • intgen Computes generation intervals by sex and birth year of the progeny
  • intgend Computes generation intervals in days, by sex and birth year of the progeny
  • meuw Compute inbreeding coefficients of all individuals in a population with the method described by Meuwissen and Luo (1992)
  • vanrad Compute inbreeding coefficients of all individuals in a population with the method described by Meuwissen and Luo (1992)
  • grain Computes ancestral and partial inbreeding by simulation and gene dropping
  • prob_orig Computes the probabilities of gene origin for a reference population
  • contribution Détermine la contribution cumulée d’une série d’ancêtres donnés à une population de référence définie par une liste ou par le sexe et les années de naissance
  • contribution with the ancestor file
  • Segreg Simulates the segregation of founder alleles in the population
  • Etr Computes the probabilities of gene origins
  • par Computes the relationship matrix of a large population
  • par2 with file group Computes the relationship matrix of a large population
  • par2 with parameters
  • par3
  • parente Searches for ancestors common to a given group of individuals or common to the parents of the individuals of this group
• QTL Detection
  • QTL - Linkage Analysis with Microsatellites for single and multiple real and precorrected traits
  • QTL - Linkage Analysis with Microsatellites for single real trait with a model description (nuisances effects)
  • QTL - Linkage Analysis, Linkage Disequilibrium and LDLA with SNP for single real trait with a model description (nuisances effects)
• EQTL Detection
  • EQTL - Linkage Analysis with Microsatellites for single and multiple real and precorrected data
  • EQTL - Linkage Analysis with Microsatellites for single real data with a model description (nuisances effects)
  • EQTL - Linkage Analysis, Linkage Disequilibrium and LDLA with SNP for single real data with a model description (nuisances effects)
• Genomic Selection
  • GS3 Estimates fixed and random effects, breeding values and SNP effects for genomic selection
  • Simple BayesCpi (QTLMap format) Estimates SNP effects
  • Simple BayesCpi
• Selective Sweeps Detection
  • Pool HMM Estimating allele frequencies and detecting selective sweeps using NGS