Alternatives and similar repositories for mushi:

Users that are interested in mushi are comparing it to the libraries listed below

• standard-aaron / palm
  Polygenic Adaptation Likelihood Method - Inferring natural selection on complex traits from whole-genome genealogies
  ☆16Updated 4 years ago
• mcveanlab / treeseq-inference
  Work for the tree sequence inference paper.
  ☆23Updated 4 years ago
• mdrasmus / argweaver
  Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)
  ☆51Updated 9 years ago
• ramachandran-lab / SWIFr
  Sweep Inference Framework (controlling for correlation)
  ☆29Updated 7 months ago
• sriramlab / SCOPE
  Scalable population structure inference
  ☆18Updated 2 years ago
• tulerpetontidae / psmc-python
  A reimplementation of a classical PSMC method in python for educational purposes
  ☆14Updated 7 months ago
• popgenmethods / pyrho
  Fast inference of fine-scale recombination rates based on fused-LASSO
  ☆47Updated this week
• jjberg2 / PolygenicAdaptationCode
  ☆20Updated 4 years ago
• lntran26 / donni
  machine learning applications for dadi
  ☆14Updated last month
• gravelLab / tracts
  A set of tools for modelling ancestry patterns along the genome.
  ☆22Updated last month
• LohmuellerLab / fitdadi
  Tools for inference of the DFE with dadi
  ☆14Updated 3 years ago
• Rosemeis / HaploNet
  Haplotype and population structure inference using neural networks.
  ☆27Updated 2 months ago
• yairf / SDS
  R code to compute the Singleton Density Score (SDS)
  ☆28Updated 8 years ago
• popgenmethods / SINGER
  Sampling and inference of genealogies with recombination
  ☆29Updated 5 months ago
• kr-colab / popvae
  genotype dimensionality reduction with a VAE
  ☆43Updated 10 months ago
• merlebehr / treeSeg
  Implementation of the treeSeg algorithm as an R package.
  ☆14Updated 2 years ago
• pkalbers / geva
  Genealogical Estimation of Variant Age (GEVA)
  ☆28Updated 3 years ago
• popgenmethods / ldpop
  Two locus likelihoods and ARGs under changing population size
  ☆13Updated 3 years ago
• CshlSiepelLab / arg-selection
  ARG-based inference of selection using deep learning
  ☆18Updated last year
• molpopgen / fwdpy11
  Forward-time simulation in Python using fwdpp
  ☆30Updated 2 months ago
• AgResearch / KGD
  Kinship (genetic relatedness) using GBS (genotyping-by-sequencing) with Depth adjustment
  ☆21Updated 2 weeks ago
• fgvieira / ngsLD
  Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework
  ☆46Updated last year
• ksiewert / BetaScan
  Genome-wide scan for balancing selection using beta statistic
  ☆28Updated last year
• MyersGroup / relate
  Software for estimating genome-wide genealogies for thousands of samples
  ☆29Updated 4 months ago
• popsim-consortium / demes-python
  Tools for describing and manipulating demographic models.
  ☆19Updated this week
• tskit-dev / tsdate
  Infer the age of ancestral nodes in a tree sequence.
  ☆20Updated this week
• mailund / admixture_graph
  Module for analysing admixture graphs
  ☆28Updated 6 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆52Updated 4 years ago
• popsim-consortium / manuscript
  PopSim consortium manuscript
  ☆7Updated 4 years ago
• rwdavies / QUILT
  QUILT: Low coverage whole genome sequence imputation with large reference panels
  ☆57Updated 3 months ago