genotype-likelihoods topic
polyRAD
Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
radiator
RADseq Data Exploration, Manipulation and Visualization using R
stackr
stackr: an R package to run stacks software pipeline
glactools
command-line tools for the management of genotype likelihoods and allele counts
ngsF
Estimation of per-individual inbreeding coefficients under a probabilistic framework
ngsLD
Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
polyploid-genotyping
SNP genotyping in polyploids
TypeTE
Genotyping of segregating mobile elements insertions
HMMploidy
A tool to calculate ploidy levels from genotype likelihoods and coverage using Hidden Markov Models