Alternatives and similar repositories for polyploid-genotyping

Users that are interested in polyploid-genotyping are comparing it to the libraries listed below

• luntergroup / smcsmc
  Demographic inference from whole genomes
  ☆13Updated 2 years ago
• weissmanlab / magic
  Minimal Assumption Genomic Inference of Coalescence
  ☆14Updated 2 years ago
• bcm-uga / pcadapt
  Performing highly efficient genome scans for local adaptation with R package pcadapt v4
  ☆42Updated 2 weeks ago
• hemstrow / snpR
  ☆30Updated 2 months ago
• danjlawson / badMIXTURE
  R package for comparing mixture solutions to similarity data, with a focus STRUCTURE like models to ChromoPainter palettes
  ☆26Updated 5 years ago
• grenaud / vgan
  Suite of tools for pangenomics built using vg
  ☆23Updated 3 weeks ago
• AgResearch / KGD
  Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment
  ☆21Updated last week
• TBooker / PicMin
  ☆11Updated 2 years ago
• bwringe / hybriddetective
  ☆14Updated 2 years ago
• champost / ABLE
  ABLE - Approximate Blockwise Likelihood Estimation
  ☆17Updated 7 years ago
• augusto-garcia / onemap
  Repository created to host the R package OneMap: software for constructing genetic maps in experimental crosses: full-sib, RILs, F2 and b…
  ☆38Updated last year
• tskit-dev / tsdate
  Infer the age of ancestral nodes in a tree sequence.
  ☆21Updated 3 weeks ago
• arthurkorte / GWAS
  ☆13Updated 4 years ago
• GonzalezLab / T-lex3
  ☆15Updated 5 years ago
• mailund / admixture_graph
  Module for analysing admixture graphs
  ☆28Updated 7 years ago
• ANGSD / NgsRelate
  ☆43Updated 4 months ago
• novikovalab / piawka
  The powerful `awk` script to calculate pi, Dxy and Fst in polyploid VCF files with mixed-ploidy groups support
  ☆28Updated 4 months ago
• ksiewert / BetaScan
  Genome-wide scan for balancing selection using beta statistic
  ☆29Updated 2 years ago
• karel-brinda / samsift
  SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  ☆23Updated 7 years ago
• lntran26 / donni
  machine learning applications for dadi
  ☆15Updated 6 months ago
• regevs / gamma_smc
  ☆20Updated last year
• kristinmlee / dmc
  Distinguishing among modes of convergent adaptation using population genomic data: statistical inference method, extensions, and examples
  ☆13Updated 6 years ago
• mcstitzer / maize_genomic_ecosystem
  ☆11Updated 3 years ago
• jmonlong / sveval
  Functions to compare a SV call sets against a truth set.
  ☆30Updated last month
• sriramlab / ArchIE
  A statistical framework for reference-free inference of archaic local ancestry
  ☆16Updated 5 years ago
• Rosemeis / emu
  EM-PCA for Ultra-low Coverage Sequencing Data
  ☆18Updated 6 months ago
• yangjl / GERP-diallel
  Research repo for Yang et al., 2017 paper.
  ☆9Updated 5 years ago
• GenisGE / evalAdmix
  ☆14Updated last year
• mhoban / haplonet
  R script to plot haplotype networks
  ☆6Updated 3 years ago
• popgenmethods / ldpop
  Two locus likelihoods and ARGs under changing population size
  ☆14Updated 4 months ago