Alternatives and similar repositories for stdpopsim

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

• tskit-dev / msprime
  Simulate genealogical trees and genomic sequence data using population genetic models
  ☆197Updated this week
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆87Updated 3 years ago
• dipetkov / eems
  Estimating Effective Migration Surfaces
  ☆105Updated last year
• mfumagalli / ngsTools
  Programs to analyse NGS data for population genetics purposes
  ☆175Updated last year
• silastittes / shiny_popgen
  Shiny apps for teaching Population Genetics
  ☆65Updated 2 years ago
• uqrmaie1 / admixtools
  ☆83Updated 2 months ago
• rajanil / fastStructure
  A variational framework for inferring population structure from SNP genotype data.
  ☆140Updated 2 years ago
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆114Updated 10 months ago
• andrewkern / popGenMachineLearningExamples
  simple examples of using supervised machine learning for population genetics inference
  ☆38Updated 7 years ago
• ksamuk / pixy
  Software for painlessly estimating average nucleotide diversity within and between populations
  ☆140Updated last week
• jpuritz / dDocent
  a bash pipeline for RAD sequencing
  ☆55Updated 7 months ago
• jade-cheng / ohana
  mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.
  ☆87Updated 4 years ago
• szpiech / selscan
  Haplotype based scans for selection
  ☆131Updated last week
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆106Updated 2 months ago
• tskit-dev / tsinfer
  Infer a tree sequence from genetic variation data.
  ☆60Updated last week
• petrelharp / local_pca
  Methods for examining PCA locally along the genome.
  ☆83Updated last year
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆172Updated 2 years ago
• bodkan / slendr
  Population genetic simulations in R 🌍
  ☆60Updated 2 weeks ago
• isaacovercast / easySFS
  Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style …
  ☆155Updated last year
• dereneaton / ipyrad
  Interactive assembly and analysis of RAD-seq data sets
  ☆77Updated 2 months ago
• rwdavies / STITCH
  STITCH - Sequencing To Imputation Through Constructing Haplotypes
  ☆83Updated 2 weeks ago
• kr-colab / locator
  deep learning prediction of geographic location from individual genome sequences
  ☆51Updated 7 months ago
• danrlu / nextflow_cheatsheet
  Tips for Nextflow and cheatsheet for channel operation
  ☆78Updated last year
• FePhyFoFum / phyx
  phylogenetics tools for linux (and other mostly posix compliant) computers
  ☆121Updated 7 months ago
• Yale-EEB723 / syllabus
  ☆22Updated 6 years ago
• halasadi / MAPS
  software for the MAPS method
  ☆24Updated 6 years ago
• tskit-dev / tskit
  Population-scale Ancestral Recombination Graph (ARG) library
  ☆169Updated last week
• stschiff / msmc
  Implementation of the multiple sequential markovian coalescent
  ☆89Updated 3 weeks ago
• tatumdmortimer / popgen-stats
  Scripts to calculate population genetics statistics
  ☆55Updated 7 years ago
• harvardinformatics / snpArcher
  Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
  ☆81Updated last week